CleanTech Biofuels, Inc. (Form: 10-K, Received: 03/29/2012 16:57:11)

UNITED STATES SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

Form 10-K

þ ANNUAL REPORT UNDER SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the fiscal year ended December 31, 2011

o TRANSITION REPORT UNDER SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the transition period from ______________ to________________

Commission file number 333-145939

CleanTech Biofuels, Inc.

(Exact Name of Registrant as Specified in Its charter)

Delaware		33-0754902
(State or other jurisdiction of incorporation or organization)		(I.R.S. Employer Identification No.)

7386 Pershing Ave., University City, Missouri		63130
(Address of principal executive offices)		(Zip Code)

(Registrant's telephone number): (314) 802-8670

Securities registered under Section 12(b) of the Exchange Act: None

Securities registered under Section 12(g) of the Exchange Act: None

Indicate by check mark if the registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act. Yes o No þ

Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or 15(d) of the Act. Yes o No þ

Indicate by check mark whether registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the past 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes þ No o

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T ( 232.405) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files). Yes o No o

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K (229.405) is not contained herein, and will not be contained, to the best of registrant’s knowledge, in definitive proxy or information statements incorporated by reference in Part III of this Form 10-K or any amendment to this Form 10-K. þ

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company. See the definitions of “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act.

(Check one):

Large accelerated filer	o	Accelerated filer	o
Non-accelerated filer	o (Do not check if a smaller reporting company)	Smaller reporting company	þ

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Act). Yes o No þ

The aggregate market value of the voting and non-voting common equity held by non-affiliates as of June 30, 2011 (the last business day of our most recently completed second quarter) - $2,594,371

As of March 23, 2012, the number of shares outstanding of the Company's common stock was 69,844,000.

DOCUMENTS INCORPORATED BY REFERENCE

CLEANTECH BIOFUELS, INC.

TABLE OF CONTENTS

PART I		PAGE
ITEM 1	Business	3
ITEM 1A	Risk Factors		11
ITEM 1B	Unresolved Staff Comments		17
ITEM 2	Properties		17
ITEM 3	Legal Proceedings		17
ITEM 4	(Removed and Reserved)		17

PART II
ITEM 5	Market for Registrant’s Common Equity, Related Stockholder Matters and Issuer Purchases of Equity Securities		18
ITEM 6	Selected Financial Data
ITEM 7	Management’s Discussion and Analysis of Financial Condition and Results of Operations		20
ITEM 7A	Quantitative and Qualitative Disclosures About Market Risk		20
ITEM 8	Financial Statements and Supplemental Data		28
ITEM 9	Changes in and Disagreements with Accountants on Accounting and Financial Disclosure		48
ITEM 9A	Controls and Procedures		48
ITEM 9B	Other Information		49

PART III
ITEM 10	Directors, Executive Officers and Corporate Governance		49
ITEM 11	Executive Compensation		51
ITEM 12	Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters		55
ITEM 13	Certain Relationships and Related Transactions and Director Independence		56
ITEM 14	Principal Accountant Fees and Services		57

PART IV.
ITEM 15	Exhibits and Financial Statement Schedules		58
	Signatures		60
	Index to Exhibits		61

Statement Regarding Forward-Looking Information

From time to time, we make written or oral statements that are “forward-looking,” including statements contained in this report and other filings with the Securities and Exchange Commission (“SEC”) and in our reports to stockholders. The Private Securities Litigation Reform Act of 1995 and Section 21E of the Securities Exchange Act of 1934, as amended, provide a safe harbor for such forward-looking statements. All statements, other than statements of historical facts, included herein regarding our strategy, future operations, financial position, future revenues, projected costs, prospects, plans, objectives and other future events and circumstances are forward-looking statements. In some cases, you can identify forward-looking statements by terminology such as “anticipates,” “believes,” “estimates,” “expects,” “intends,” “may,” “plans,” “projects,” “would,” “should” and similar expressions or negative expressions of these terms. Such statements are only predictions and, accordingly, are subject to substantial risks, uncertainties and assumptions.

Actual results or events could differ materially from the plans, intentions and expectations disclosed in the forward-looking statements we make. We caution you that any forward-looking statement reflects only our belief at the time the statement is made. Although we believe that the expectations reflected in our forward-looking statements are reasonable, we cannot guarantee our future results, levels of activity, performance or achievements. Refer to our Risk Factors section of this report for a full description of factors we believe could cause actual results or events to differ materially from the forward-looking statements that we make. These factors include:

	● our ability to raise additional capital on favorable terms, ● our ability to continue operating and to implement our business plan, ● the commercial viability of our technologies,
	● our ability to maintain and enforce our exclusive rights to our technologies,

● the demand for and production costs of various energy products made from our biomass,

● competition from other alternative energy technologies, and

● other risks and uncertainties detailed from time to time in our filings with the SEC.

Although we believe the expectations reflected in our forward-looking statements are based upon reasonable assumptions, it is not possible to foresee or identify all factors that could have a material and negative impact on our future performance. The forward-looking statements in this report are made on the basis of management’s assumptions and analyses, as of the time the statements are made, in light of their experience and perception of historical conditions, expected future developments and other factors believed to be appropriate under the circumstances.

PART I

ITEM 1. BUSINESS

The following discussion of our Company Overview and Plan of Operation should be read in conjunction with the financial statements and related notes to the financial statements included elsewhere in this report. This discussion contains forward-looking statements that relate to future events or our future financial performance. These statements involve known and unknown risks, uncertainties and other factors that may cause our actual results, levels of activity or performance to be materially different from any future results, levels of activity or performance. These risks and other factors include, among others, those listed under “Statement Regarding Forward-Looking Information.”

Company Overview

We are a development stage company focused on being a provider of: (i) cellulosic biomass derived from municipal solid waste, also known as MSW, as a feedstock for producing energy and other chemical products and (ii) recyclables (metals, plastics, glass) from the MSW.

We are the exclusive licensee in the United States and Canada of patented technology in the United States that we refer to as our Biomass Recovery Process that cleans and separates MSW and generates a clean, homogeneous biomass feedstock that we believe can be converted into various energy products. Our license permits us to use the biomass we derive from MSW to produce all energy products. In addition, we own the patent for a pressurized steam classification technology originally developed by the University of Alabama Huntsville that we refer to as our PSC technology. The PSC technology is the underlying technology upon which the Biomass Recovery Process was based. Prior to March 2011, we had licensed the PSC technology to Bio-Products International, Inc. (“Bio-Products”) pursuant to the terms of a settlement agreement we entered into with Bio-Products in March 2009, whereby, in addition to a customary mutual release, Bio-Products entered into a covenant not to sue whereby Bio-Products and its related parties agreed to permit us to use the Biomass Recovery Process technology worldwide, for any product that we desire and with no royalty due to Bio-Products.

We were originally incorporated in 1996 as Long Road Entertainment, Inc., and were formed to operate as a holding company for businesses in the theater, motion picture and entertainment industries. We ceased conducting that business in 2005 and were dormant until the fall of 2006, at which time our founder and then controlling stockholder decided to pursue the sale of the company. In anticipation of that sale, we changed our name to Alternative Ethanol Technologies, Inc.

On March 27, 2007, we entered into an Agreement and Plan of Merger and Reorganization in which we agreed to acquire SRS Energy, Inc., a Delaware corporation that at that time was seeking to commercialize various technologies for the processing of waste materials into usable products. We consummated the merger on May 31, 2007 resulting in SRS Energy becoming our wholly-owned subsidiary. Effective August 2, 2007, we changed our name to CleanTech Biofuels, Inc.

We have no operating history as a producer of biomass feedstocks or any energy products and have not constructed any operating plants to date. We have not earned any revenues to date and our current capital and other existing resources are not sufficient to fund the implementation of our business plan or our required working capital. We will require substantial additional capital to implement our business plan and we may be unable to immediately obtain the capital required to continue operating.

Plan of Operation

Our focus is to secure sufficient capital to fund our current working capital requirements and the construction of a commercial plant as described further in this section. We currently do not have sufficient capital to continue operations. All of our developments/projects require a significant amount of capital that we currently do not have. While we continue to aggressively pursue capital, we have not had recent success securing meaningful amounts of financing. As a result, we can provide no assurance that we will secure any capital in the immediate time frame required and the failure to do so will likely result in an inability to continue operations.

Our company was initially conceived as a fully-integrated producer of cellulosic ethanol from MSW. Based on our investigation and acquisition of new technologies and research and development of our existing technologies in 2008, we re-focused our business to the commercialization of our Biomass Recovery Process technology for cleaning and separating MSW into its component parts and initiated a plan to consolidate the ownership and/or rights to use intellectual property around this technology. The technology is currently in use by another operator in a commercial setting in Australia. As a result, we believe this technology is ready for commercial implementation in the United States and elsewhere. In furtherance of our new focus, we are currently in the process of raising capital to design and build a commercial biomass recovery plant to provide biomass feedstock for customer evaluation and trial purchases. Initially, the biomass feedstock output will be sold or provided to electric utilities, power and steam producers, and biofuel research firms for evaluation. In addition to this capital raise for plant development, the Company is also working towards licensing and/or developing potential commercial projects as they present themselves. All of our developments plan to focus on cleaning and separating MSW into its component parts in order to obtain: (i) a homogenous feedstock of cellulosic biomass for producing energy and other chemical products and (ii) recyclable products (metals, plastics).

Biomass Feedstock Production

The Company plans to design and build a commercial biomass recovery plant to provide biomass feedstock for customer evaluation and trial purchases. Initially, the biomass feedstock output will be sold or provided to electric utilities, power and steam producers, and biofuel and chemical research firms for evaluation. In addition to research and development, the Company is also working towards licensing and/or developing potential commercial projects.

We completed construction of a small test vessel in Kentucky and, beginning in April 2009, this vessel has processed approximately 12 tons of MSW into approximately 4-5 tons of biomass. We have provided the biomass produced during this testing phase to a number of fuel producers who are evaluating whether they can use our biomass as a feedstock for their technologies. In July 2010, we entered into an agreement with Fiberight to install this test vessel at Fiberight’s cellulosic ethanol pilot plant in Lawrenceville, Virginia. Fiberight is continuing to evaluate alternative technologies to provide feedstock for their process, which we expect they will complete during the second quarter 2012. If and when installed, our vessel is expected to produce cellulosic biomass feedstock for Fiberight’s Targeted Fuel Extraction process. We expect such production should further validate our licensed Biomass Recovery Process. Additionally, we will have access to biomass produced at the Lawrenceville plant for delivery to other companies interested in testing it as feedstock in their conversion technologies.

We are also seeking to develop a plant in a major metropolitan area. We are working to develop one or more locations where waste collected would be processed using our technology and the biomass produced used to create heat and/or power.

In addition to the developments we are currently contemplating, other development opportunities are presented to us and we evaluate those potential developments. Upon operating a plant and after refining our know-how with respect to implementation of the technology, we intend to seek to partner with waste haulers, landfill owners and municipalities to implement the technology in our licensed territories.

The further development of commercial plants and/or implementation of the licensing of our technology described above will require significant additional capital, which we currently do not have. We cannot provide any assurance that we will be able to raise this additional capital. While we anticipate that financing for the commercial biomass recovery plant and these other potential projects could also be provided in part via tax exempt bond financing or through the use of loan guarantees from local, state and federal authorities, we have not secured any such financing and there can be no assurance that we will be able to secure any such financing.

Bio-Fuel and Bio-Chemical Joint Testing/Research

As soon as we are able to process MSW into biomass through our future biomass recovery plant and/or in future commercial vessels, we plan to enter into joint research agreements with companies looking to process biomass in their system(s) for various types of energy and chemical production. This testing and research will provide possible revenue streams, projects and additional opportunities for use of our biomass.

In February 2012, we entered into a Confidentiality Agreement and Material Transfer Agreement with Sweetwater Energy, Inc., (“Sweetwater”) a renewable energy company with patent-pending technology to produce sugars from several types of biomass for use in the biofuel, biochemical and bioplastics markets. Cleantech has agreed and has coordinated with the facility in Coffs Harbor, Australia to ship 10 pounds of biomass produced at the Coffs Harbor facility to the Sweetwater lab for testing. The shipment is expected to arrive in late-March or early-April 2012.

In June 2011, we entered into a Confidential Disclosure and Sampling Agreement with Novozymes North America, Inc., a developer of industrial enzymes, microorganisms, and biopharmaceutical ingredients for conversion into a variety of energy and chemical products. In July 2011, we supplied a sample of our biomass product for testing in their enzymatic hydrolysis process. Some initial testing was completed during the 3 rd Quarter of 2011. We expect further testing to occur upon securing the requisite financing.

New Technologies; Commercializing Existing Technologies

Because of our unique ability to produce a clean, homogenous biomass feedstock, we are frequently presented with the opportunity to partner with or acquire new technologies. In addition to developing our current technologies, we will continue to add technologies to our suite of solutions that complement our core operations. We believe that our current technologies and aspects of those in development will enable us to eventually expand our business to use organic material from other waste streams such as municipal bio-solids from waste water facilities and animal waste for fuel production.

To commercialize our technology, we intend to:

●	construct and operate a commercial plant that: (i) processes MSW into cellulosic biomass for conversion into energy or chemical products and (ii) separates recyclables (metals, plastics, glass) for single-stream recycling;

●	identify and partner with landfill owners, waste haulers and municipalities to identify locations suitable for our technology; and

●	pursue additional opportunities to implement our technology in commercial settings at transfer stations and landfills in our licensed territories.

Our ability to implement this strategy will depend on our ability to raise significant amounts of additional capital and to hire appropriate managers and staff. Our success will also depend on a variety of market forces and other developments beyond our control.

Industry Overview

There are two types of MSW Disposal:

●	Municipal Solid Waste Landfills (“MSWLFs”) - includes municipal solid waste, commercial waste, industrial waste, construction and demolition debris, and bioreactors.

●	Mass Burn/Incineration Plants

Municipal Solid Waste Landfills

MSWLFs primarily receive household waste and commercial waste. MSWLFs can also receive non-hazardous sludge, industrial solid waste, and construction and demolition debris. All MSWLFs must comply with various federal, state and local laws and regulations.

Disposing of waste in a landfill involves burying waste, and this remains a common practice in most countries. Historically, landfills were often established in disused quarries, mining voids or borrow pits. A properly-designed and well-managed landfill can be a hygienic and relatively inexpensive method of disposing of waste materials. Older, poorly-designed or poorly-managed landfills can create a number of adverse environmental impacts such as wind-blown litter, attraction of vermin, and generation of liquid leachate. Another common byproduct of landfills is gas (mostly composed of methane and carbon dioxide), which is produced as organic waste breaks down anaerobically. This gas can create odor problems, kill surface vegetation, and contributes to global warming.

Waste haulers or municipalities pay tipping fees, or gate rates, on a per ton basis to dispose of garbage at a landfill. Gate rates operate in a manner similar to the published prices for airline tickets or hotels, before discounts or contract prices (which could be higher or lower) are considered. The gate rate is the true daily market value of the tipping fee. The average tipping fee in the United States has risen consistently from $8.20 per ton in 1985 to $42.08 in 2006 and continues to increase.

Mass Burn/Incineration Plants

Mass Burn - Mass burn is combusting MSW generally without any pre-processing or separation. The resulting steam is employed for industrial uses or for generating electricity. Mass burn facilities are sized according to the daily amount of solid waste they expect to receive. Most mass burn plants can remove non-combustible steel and iron for recycling before combustion using magnetic separation processes. Other non-ferrous metals can be recovered from the leftover ash.

Waste-to-Energy (WTE) Plants - Current operating WTE plants burn MSW in a controlled environment to create steam or electricity. Through this process the volume of solid waste is reduced by about 90%.

Modular Incinerators - Modular incinerators are small mass burn plants, with a capacity of 15 to 100 tons per day. The boilers for modular incinerators are built in a factory and shipped to the WTE site, rather than being built on the WTE site itself. The advantage of a modular WTE incinerator is flexibility. If more capacity is needed, modular WTE units can be added. These facilities are used primarily by small communities and industrial sites. Costs limit the use of this technology because the return on investment in terms of energy produced over time is much lower than in mass burn plants.

Refuse-Derived Fuel (RDF) Plants - RDF plants process solid waste before it is burned. A typical plant will remove non-combustible items, such as glass, metals and other recyclable materials. The remaining solid waste is then shredded into smaller pieces for burning. RDF plants require significantly more sorting and handling than mass burn, but can recover recyclables and remove some potentially environmentally harmful materials prior to combustion. RDF can be burned in power boilers at factories or even at large housing complexes. Sometimes RDF materials are "densified" (compacted at high pressure) to make fuel pellets. The "pellet fuel" may also include various sludges, by-products of municipal or industrial sewage treatment plants.

MSW contains a diverse mix of waste materials, some benign and some very toxic. Effective environmental management of MSW plants aims to exclude toxics from the MSW-fuel and to control air pollution emissions from the WTE plants. Toxic materials include trace metals such as lead, cadmium and mercury, and trace organics, such as dioxins and furans. Such toxins pose an environmental problem if they are released into the air with plant emissions or if they are dispersed in the soil and allowed to migrate into ground water supplies and work their way into the food chain. The control of such toxics and air pollution are key features of environmental regulations governing MSW fueled electric generation.

U.S. EPA rules are among the most stringent environmental standards for WTE facilities in the world. These rules mandate that all facilities use the most modern air pollution control equipment available to ensure that WTE smokestack emissions are as clean as possible, and are safe for human health and the environment.

Burning any fuel, including MSW, can produce a number of pollutants, such as carbon monoxide, sulfur dioxide, and fine particles containing heavy metals. Other toxic organic compounds, such as dioxins, are also potential emissions from any combustive activity where certain chemical compounds are present, a situation that could take place in the WTE process. Air emission control devices in a WTE facility usually include:

●	Dry Scrubbers – these "wash" the air emissions from the WTE process (called the gas stream) and remove any acidic gases by passing the gas stream through a liquid.

●	Electrostatic Precipitators (ESP) – these use high voltage electricity to remove up to 98% of all particles remaining in the gas stream after passing through the scrubbers, including any heavy metal particles.

●	Fabric Filters (baghouses) – these consist of a series of nearly two thousand fabric bags made of heat-resistant material which filter remaining particles from the gas stream. This includes any large concentrations of condensed toxic organic compounds (such as dioxins) and heavy metal compounds.

Incinerators and RDF processors are paid tipping fees for the garbage that they accept. Typically, these fees are more costly than the fees paid to landfill operators. Average tipping fees are lower at landfills than at combustion facilities, largely because of the high capital and operating costs at combustion facilities.

Environmental Matters

We believe our company will be subject to international, federal, state and local laws and regulations with regard to air and water quality, hazardous and solid waste disposal and other environmental matters upon commercial operations. There is always a risk that the federal agencies may enforce certain rules and regulations differently than state and local environmental administrators. Federal, state and local rules are subject to change, and any such changes could result in greater regulatory burdens on plant operations. We could also be subject to environmental or nuisance claims from adjacent property owners or residents in the areas arising from possible foul smells or other air or water discharges from the plant. We do not know the potential cost of these requirements or potential claims. Environmental laws and regulations that may affect us in the future may include, but are not limited to:

●

The Clean Air Act, as well as state laws and regulations impacting air emissions, including State Implementation Plans related to existing and new national ambient air quality standards for ozone and particulate matter. Owners and/or operators of air emission sources are responsible for obtaining permits and for annual compliance and reporting.

●	The Clean Water Act which requires permits for facilities that discharge wastewaters into the environment.

●	The Solid Waste Disposal Act, as amended by the Resource Conservation and Recovery Act, which requires certain solid wastes, including hazardous wastes, to be managed pursuant to a comprehensive regulatory regime.

●	The National Environmental Policy Act, which requires federal agencies to consider potential environmental impacts in their decisions, including siting approvals.

Government Approvals

The Company is not subject to any government approvals or oversight for its current operations other than normal corporate governance and taxes. Once we begin developing commercial production facilities, however, we will be subject to multiple federal, state and local environmental laws and regulations, such as those described above and for employee health and safety. In addition, some of these laws and regulations will require our facilities to operate under permits that are subject to renewal or modification. A violation of these laws and regulations or permit conditions can result in substantial fines, natural resource damages, criminal sanctions, permit revocations and/or facility shutdowns.

Our Technology

We believe we can convert MSW into cellulosic material using our Biomass Recovery Process, which can then be used by a variety of third party technologies as a feedstock to process that cellulosic material into a variety of energy and chemical products.

Biomass Recovery Process

MSW contains valuable resources if they can be recovered economically. Waste haulers often bring unsorted waste by truck to MRFs for sorting and removal of selected materials prior to disposal in sanitary landfills. To date, however, the amounts of materials recovered are relatively small, typically on the order of approximately 25 percent of the total volume of waste.

The PSC technology was developed at the University of Alabama, Huntsville and improved by Anthony Noll into the technology we refer to as the Biomass Recovery Process. The process separates curbside MSW into organic and inorganic materials using a patented and proprietary process that involves a unique combination of steam, pressure and agitation. The separation is accomplished by placing waste material in a rotating pressure vessel, or autoclave. In the autoclave, the material is heated to several hundred degrees, which sterilizes the waste material, while the pressure and agitation cause a pulping action. This combination is designed to result in a large volume reduction, yielding the following two sterilized resource streams for further manufacturing of new products:

●	Cellulosic biomass, a decontaminated, homogeneous feedstock that we expect will represent approximately 50 to 60 percent of the incoming MSW and will be suitable for conversion to multiple energy or chemical products.

●	Separated recyclables (steel cans and other ferrous materials, aluminum cans, plastics, and glass), which we expect will represent about 25 percent of the MSW input and are sorted and can be sold to recyclers.

The process also creates residual waste (fines, rocks, soil, textiles and non-recyclable fractions), which we expect will represent the remaining 15 to 25 percent of the MSW input. We will not be able to recover any value in this residual waste. We will be required to deliver this waste to landfills and incur the tipping fees expense.

The process is currently working in a commercial plant in Coffs Harbor, Australia and has been in operations for over three years. We believe that our process represents a significant improvement over other autoclave technologies currently in use because of:

●	the relationship between agitation of the waste material, moisture, and the temperature and pressure of steam in the vessel uses less energy while obtaining a cleaner biomass resource;

●	the method of introduction of steam into the autoclave vessel, the pressure range, along with the method of full depressurization, and treatment of the steam being vented from the process to prevent air pollution make our process more environmentally friendly than any other means to handle MSW;

●	the method of mixing the heat and steam with the waste uniformly throughout the vessel create a homogenous feedstock for fuel production; and,

●	the direct and critical correlation between the length and diameter of the vessel, internal flighting and the total tonnage of waste to be processed for proper mixing and product yield.

Principal Products or Services and their Markets

If we determine that our licensed technologies are commercially viable and we are able to raise a significant amount of additional capital, we may be in a position to begin to license and/or enter into long-term contracts with municipalities, solid waste haulers, and operators of landfills and materials recovery facilities to process a large portion of their waste stream into biomass and recyclable materials.

Energy/Chemicals

We expect the primary product we will sell will be biomass from our Biomass Recovery Process to be used for conversion to energy or chemical products. We believe our biomass can be used in multiple varieties of energy production systems. We expect the uses for our biomass to expand as new energy production technologies are developed.

MSW Processing Services

We believe that the opportunity to help communities, haulers and landfill managers reduce the amount of material transported and deposited in landfills is large and growing. The Resource Conservation and Recovery Act of 1991, referred to as RCRA, requires landfills to install expensive liners and other equipment to control leaching toxics. Due to the increased costs and expertise required to manage landfills under RCRA, many small, local landfills closed during the 1990’s. Larger regional landfills were built requiring increased transportation costs for the waste haulers. As a result, landfill space is increasingly scarce and disposal costs have been increasing.

Currently, landfill operators charge a tipping fee to deliver MSW to a landfill, waste-to-energy facility, recycling facility, transfer station or similar facility. Tipping fees vary widely based on geographic location and the number of available places to dispose of MSW in a given location. Because of the increasing cost pressures on waste haulers and based on current tipping fee pricing, we believe we will be able to negotiate a payment of part of their tipping fee from waste haulers who deliver MSW to us for processing that would range from as low as $15 per ton in some central parts of the country to over $80 per ton in the Northeast and some parts of the Southeast. The availability of tipping fees at favorable rates will be a key component of our business.

Recyclable Byproducts

We anticipate that our Biomass Recovery Process will generate other recyclable byproducts from the processing of MSW, such as aluminum, metals, tin, steel, glass and plastic (typically 20 to 25 percent of the total waste stream). The markets for these recovered products are volatile and subject to rapid and unpredictable market changes making it impossible at this time to provide estimated per ton cost to revenue information.

Sources and Availability of Raw Materials

The emergence of technologies to convert MSW to energy or chemicals is opening new opportunities. What was once perhaps the greatest sanitation and health challenge for communities may now become an economic and environmental asset. Instead of adding to landfills already nearing capacity limits, converting MSW to biomass can provide one of the building blocks to a more sustainable energy future.

Americans produce more than 400 million tons of MSW annually. About 30 percent of this waste is currently recovered and recycled. We estimate that approximately up to an additional 50 percent could potentially be recovered. As various waste processing technologies are refined, competition for this future resource will intensify. As a result, it will be important for us to attempt to lock up as much of it as possible through long-term feedstock supply agreements with operators of materials recovery facilities and landfills.

Intellectual Property Terms

Biomass North America Licensing, Inc.

On September 15, 2008, the Company consummated the acquisition of Biomass North America Licensing, Inc. (“Biomass”) pursuant to a merger between Biomass and a wholly-owned subsidiary of the Company (with Biomass as the surviving subsidiary of the Company) in accordance with an Agreement and Plan of Merger by and between the Company and Biomass. By virtue of the merger, the Company acquired a license agreement pursuant to which the Company holds a license in the United States and Canada to use patented technology owned by Biomass North America, LLC, the former parent of Biomass (the “Licensor”), to clean and separate MSW (the “Biomass Recovery Process”). In July 2010, the United States Patent and Trademark Office issued US patent number 7,745,208 for this process (the “BRP Patent”).

The license requires that the Company pay a royalty in the amount of $1.00 per ton of bone-dry biomass produced using the Biomass Recovery Process. The license agreement is for a term of 21 years or the life of any patent issued for the Biomass Recovery Process. The Company has an exclusive license in the United States and Canada to use the Biomass Recovery Process, except that a principal owner of the Licensor has the right of first offer to manage and operate any project commenced using the licensed technology within 100 miles of the City of Chicago, Illinois. The license agreement further provides that the Company and the Licensor will work in good faith to complete a commercial development in the City of Chicago using the Biomass Recovery Process.

PSC Patent

The Company owns U.S. Patent No. 6,306,248 (the “PSC Patent”), which is the underlying technology upon which the BRP Patent is based. The Company acquired the PSC Patent on October 22, 2008, pursuant to a Patent Purchase Agreement with WWT. The Patent is the basis for the pressurized steam classification technology that cleans and separates MSW into its component parts, which we refer to as the PSC technology. The Company is now a licensor to Bio-Products for this patent. Bio-Products is the exclusive licensee of the PSC technology (but not the Biomass Recovery Process) and has the right to sublicense the PSC technology to any party. Under the Master License Agreement, we are entitled to be paid 5% of any revenue derived by Bio-Products from the use of the technology and 40% of any sublicensing fees paid to Bio-Products for the use of the technology. The Master License Agreement is for a term of 20 years that commenced on August 18, 2003. On September 22, 2010, the Company sent a Notice of Breach to the licensee of our PSC Patent. We received a response from the licensee on November 5, 2010. In February 2011, we became aware that the licensee effected a transfer of the license in violation of the License Agreement. As a result, on March 21, 2011, we sent a notice of termination to the licensee and the transferee terminating the License Agreement. On August 5, 2011, the Company filed a demurrer requesting that the court dismiss the case on the grounds that Mr. Vande Vegte lacks standing to pursue a claim concerning the license and that the claim raised in the complaint is not ripe. On December 8, 2011, the demurrer to dismiss Cleantech was granted. In October 2011, a Cross-Complaint was filed by Clean Conversion Technologies, Inc. (“CCT”) and Michael Failla v. Cleantech Biofuels, Inc. CCT is seeking that the Company’s termination of the License Agreement is void. Additionally, CCT has filed suit v. Cleantech and Steve Vande Vegte alleging anti-trust violations. On March 26, 2012, the Company filed a motion to dismiss. The hearing is currently set for May 7, 2012.

Employees

The Company currently has two full-time employees, its Chief Executive Officer, Edward P. Hennessey, Jr. and its Chief Financial Officer, Thomas Jennewein.

Access to SEC Filings

Interested readers can access, free of charge, all of our filings with the SEC and any amendments to those reports filed or furnished pursuant to Section 13(a) or 15(d) of the Securities Exchange Act of 1934, as amended, through the About Us/Investor Relations/SEC Filings section of our website at www.cleantechbiofuels.net as soon as reasonably practicable after we electronically file such materials with, or furnish them to, the SEC. We will also provide a copy of these documents, free of charge, to any stockholder upon written request addressed to: CleanTech Biofuels, Inc., 7386 Pershing Ave, University City, MO 63130.

ITEM 1A. RISK FACTORS

You should carefully consider the following risk factors and other information contained in this annual report on Form 10-K when evaluating our business and financial condition. Additional risks not presently known to us and risks that we currently deem immaterial may also impair our business operations.

Risks Related to Our Business

We need to obtain significant additional capital to fund our current operations and complete the implementation of our business plan, and the failure to secure additional capital will prevent us from commercializing our technology and executing our plan of operation.

We do not currently have enough cash to fund our operations. If we are not able to obtain additional financing in the immediate future, we will be required to delay our development until such financing becomes available and may be required to cease operations. In addition, in order to fund the development of our business plan, we will be required to:

●	obtain additional debt or equity financing,

●	secure significant government grants, and/or

●	enter into a strategic alliance with a larger energy or chemical company to provide funding.

The amount of funding needed to complete the development of our business plan will be very substantial and may be in excess of the amount of capital we are able to raise. We are identifying the sources for the additional financing that we will require, but currently do not have binding commitments from any third parties to provide this financing. Our ability to obtain additional funding will be subject to a number of factors, including market conditions, acceptance of our business plan, the quality of our biomass and investor sentiment. These factors may make the timing, amount, terms and conditions of additional funding unattractive. For these reasons sufficient funding, whether on terms acceptable to us or not, may not be available. If we are unable to obtain sufficient financing on a timely basis, the development of our technology, facilities and/or products could be delayed and we could be forced to limit or terminate our operations altogether. Further, any additional funding that we obtain in the form of equity will reduce the percentage ownership held by our existing shareholders.

We have no operating experience and may not be able to implement our business plan.

As an early stage company, there is no material operating history upon which to evaluate our business and prospects. We do not expect to commence any significant operations until we test and refine information from a commercial plant for biomass production and/or develop or license an operating facility. As a result, we expect to sustain losses without corresponding revenues, which would result in the Company incurring a net operating loss that will increase continuously for the foreseeable future. We cannot provide any assurance that we will be profitable in any given period or at all.

In addition, we currently have only two full-time employees, our Chief Executive Officer and Chief Financial Officer, each of whom spend at least 40 hours a week on our business. Collectively, they have less experience in operating an alternative energy company compared to many of our competitors. Moreover, given our newness and the rapid changes in the industry, we face challenges in planning and forecasting accurately. Our lack of expertise and resources may have a negative impact on our ability to implement our strategic plans, which may result in our inability to commence meaningful operations, achieve profitable operations or otherwise succeed in other aspects of our business plan.

Our Biomass Recovery Process technology may have design and engineering issues that may increase the costs of using the technology.

The Biomass Recovery Process technology involves the use of a rotating pressure vessel, or autoclave, to combine heat, pressure and agitation to convert MSW into biomass. Although technologies that involve the separation and processing of MSW using large-scale autoclaves have not been widely adapted in commercial applications, a vessel using this process is currently operating in Australia. We have completed a small scale research and testing vessel that initially processed MSW for testing purposes.

Although we believe the autoclaves will operate properly on a commercial scale, we may encounter design and engineering problems when we try to implement this technology on a large-scale for biomass and energy production. Any design, engineering or other issue may cause delays, increase production and development costs and require us to shut down our operation.

We may not have sufficient legal protection of our technologies and other proprietary rights, which could result in the loss of some or all of our rights or the use of our intellectual properties by our competitors.

Our success depends substantially on our ability to use our owned and/or licensed technologies and to keep our licenses in full force, and for us and our technology licensor to maintain our patents, maintain trade secrecy and not infringe the proprietary rights of third parties. We cannot be sure that the patents of others will not have an adverse effect on our ability to conduct our business. Further, we cannot be sure that others will not independently develop similar or superior technologies, duplicate elements of our technologies or design around them. Even if we are able to obtain or license patent protection for our process or products, there is no guarantee that the coverage of these patents will be sufficiently broad to protect us from competitors or that we will be able to enforce our patents against potential infringers. Patent litigation is expensive, and we may not be able to afford the costs. Third parties could also assert that our process or products infringe patents or other proprietary rights held by them.

We also rely on trade secrets, proprietary know-how and technology that we will seek to protect, in part, by confidentiality agreements with our prospective joint venture partners, employees and consultants. We cannot be sure that these agreements will not be breached, that we will have adequate remedies for any breach, or that our trade secrets and proprietary know-how will not otherwise become known or be independently discovered by others.

We will be dependent on our ability to negotiate favorable feedstock supply and biomass off-take agreements.

In addition to proving and commercializing our technology, the viability of our business plan will depend on our ability to develop long-term supply relationships with municipalities, municipal waste haulers or operators of material recovery facilities, also known as MRFs, and landfills to provide us with the necessary waste streams on a long-term basis. We also will depend on these haulers, operators and facilities to take residual waste streams from our plants and to deliver or accept these streams for land filling. We currently have no such relationships or agreements. If we are unable to create these relationships and receive supply agreements on terms favorable to us we may not be able to implement our business plan and achieve profitability.

We may not be able to attract and retain management and other personnel we need to succeed.

We currently have two full-time employees, our Chief Executive Officer and Chief Financial Officer. As a result, part of our success depends on our ability to recruit senior management and other key technology development, construction and operations employees. We cannot be certain that we will be able to attract, retain and motivate such employees. The inability to hire and retain one or more of these employees could cause delays or prevent us from implementing our business strategy. The majority of our new hires could be engineers, project managers and operations personnel. There is intense competition from other companies and research and academic institutions for qualified personnel in the areas of our activities. If we cannot attract and retain, on acceptable terms, the qualified personnel necessary for the development of our business, we may not be able to commence operations or grow at an acceptable pace.

We incur significant costs as a result of being a public company.

As an operating public company, we are incurring significant legal, accounting and other expenses and our corporate governance and financial reporting activities are more time-consuming. The Sarbanes-Oxley Act of 2002, as well as rules subsequently implemented by the Securities and Exchange Commission, has required changes in corporate governance practices of public companies. For example, as an operating public company, we are required to have independent directors, create board committees and approve and adopt policies regarding internal controls and disclosure controls and procedures. In addition, we are incurring significant additional costs associated with our public company reporting requirements. These rules and regulations could make it more difficult and more expensive for us to obtain director and officer liability insurance and we may be required to accept reduced policy limits and coverage or incur substantially higher costs to obtain the same or similar coverage. As a result, it may be more difficult for us to attract and retain qualified persons to serve on our board of directors or as executive officers.

Our failure to adequately adhere to the established corporate governance practices or the failure or circumvention of our controls and procedures could seriously harm our business.

Compliance with the evolving corporate governance practices has taken a significant amount of management time and attention, particularly with regard to disclosure controls and procedures and internal control over financial reporting. Although we have reviewed our disclosure and internal controls and procedures in order to determine whether they are effective, our controls and procedures may not be able to prevent errors or frauds in the future. Faulty judgments, simple errors or mistakes, or the failure of our personnel to adhere to established controls and procedures may make it difficult for us to ensure that the objectives of the control system are met. A failure of our controls and procedures to detect other than inconsequential errors or fraud could seriously harm our business and results of operations.

Our senior management’s limited experience managing a publicly traded company diverts management’s attention from operations and could harm our business.

Our management team has limited experience managing a publicly traded company and complying with federal securities laws, including compliance with disclosure requirements on a timely basis. Our management is required to design and implement appropriate programs and policies in response to increased legal, regulatory compliance and reporting requirements, and any failure to do so could lead to the imposition of fines and penalties and harm our business.

Risks Related to our Industry

As a new small company, we will be at a competitive disadvantage to most of our competitors, which include larger, established companies that have substantially greater financial, technical, manufacturing, marketing, distribution and other resources than us.

The alternative energy and waste hauling/landfill industries in the United States are highly competitive and continually evolving as participants strive to distinguish themselves. Competition is likely to continue to increase with the emergence and commercialization of new alternative energy technologies. If we are not successful, we will not be able to compete within these industries. Moreover, the success of alternative energy generation technologies may cause larger, conventional energy companies with substantial financial resources to enter the alternative energy industry. These companies, due to their greater capital resources and substantial technical expertise, may be better positioned to develop and exploit new technologies. Our inability to respond effectively to our competition could result in our inability to commence meaningful operations, achieve profitable operations or otherwise succeed in other aspects of our business plan.

Our success may be dependent on continued high energy prices.

Prices for energy can vary significantly over time and decreases in price levels could adversely affect our profitability and viability. Worldwide energy prices are subject to a myriad of factors almost all of which are completely beyond our ability to control. Frequently, unforeseen events can have a dramatic impact on the price paid for energy. Negative changes in energy prices could cause our business model to be unviable and our technology worthless.

Waste processing and energy production is subject to inherent operational accidents and disasters from which we may not be able to recover, especially if we have only one or a very small number of facilities.

Our anticipated operations would be subject to significant interruption if any of our potential facilities experience a major accident or are damaged by severe weather or other natural disasters. In particular, processing waste and producing energy products is subject to various inherent operational hazards, such as equipment failures, fires, explosions, abnormal pressures, blowouts, transportation accidents and natural disasters. Some of these operational hazards may cause personal injury or loss of life, severe damage to or destruction of property and equipment or environmental damage, and may result in suspension of operations and the imposition of civil or criminal penalties. Currently we do not have any insurance to cover those risks. We intend to seek insurance appropriate for our business before we commence significant operations. The insurance that we plan to obtain, if obtained, may not be adequate to cover fully the potential operational hazards described above.

Alternative technologies could make our business obsolete.

Even if our technology currently proves to be commercially feasible, there is extensive research and development being conducted in alternative energy sources. Technological developments in any of a large number of competing processes and technologies could make our technology obsolete and we have little ability to manage that risk.

Risks Related to Government Regulation and Subsidization

Enforcement of energy policy regulations could change.

Energy policy in the United States is evolving rapidly. Over the last decade or so, the United States Congress has passed separate major pieces of legislation addressing energy policy and related regulations. We anticipate that energy policy will continue to be a very important legislative priority on a national, state and local level. As energy policy continues to evolve, the existing rules and regulations that benefit our industry may change. It is difficult, if not impossible, to predict changes in energy policy that could occur on a federal, state or local level in the future. The elimination of or a change in any of the current rules and regulations could create a regulatory environment that prevents us from developing a commercially viable or profitable business.

Costs of compliance may increase with changing environmental and operational safety regulations.

As we pursue our business plan, we will become subject to various federal, state and local environmental laws and regulations, including those relating to the discharge of materials into the air, water and ground, the generation, storage, handling, use, transportation and disposal of hazardous materials, and the health and safety of our employees. In addition, some of these laws and regulations require our contemplated facilities to operate under permits that are subject to renewal or modification. These laws, regulations and permits can often require expensive pollution control equipment or operational changes to limit actual or potential impacts to the environment. A violation of these laws and regulations or permit conditions can result in substantial fines, natural resource damages, criminal sanctions, permit revocations and/or facility shutdowns.

Furthermore, we may become liable for the investigation and cleanup of environmental contamination at any property that we would own or operate and at off-site locations where we may arrange for the disposal of hazardous substances. If these substances have been or are disposed of or released at sites that undergo investigation and/or remediation by regulatory agencies, we may be responsible under CERCLA, or other environmental laws for all or part of the costs of investigation and/or remediation, and for damages to natural resources. We may also be subject to related claims by private parties alleging property damage and personal injury due to exposure to hazardous or other materials at or from those properties. Some of these matters may require expending significant amounts for investigation, cleanup, or other costs.

In addition, new laws, new interpretations of existing laws, increased governmental enforcement of environmental laws, or other developments could require us to make additional significant expenditures. Continued government and public emphasis on environmental issues can be expected to result in increased future investments for environmental controls at any future production facility. Present and future environmental laws and regulations applicable to MSW processing and energy production, more vigorous enforcement policies and discovery of currently unknown conditions may require substantial expenditures that could have a material adverse effect on the results of our contemplated operations and financial position.

The hazards and risks associated with processing MSW and producing and/or transporting various energy or chemical products (such as fires, natural disasters, explosions, and abnormal pressures and blowouts) may also result in personal injury claims or damage to property and third parties. As protection against operating hazards, we intend to maintain insurance coverage against some, but not all, potential losses. We could, however, sustain losses for uninsurable or uninsured risks, or in amounts in excess of existing insurance coverage. Events that result in significant personal injury or damage to our property or third parties or other losses that are not fully covered by insurance could have a material adverse effect on the results of our contemplated operations and financial position.

Risks related to our Common Stock and Stock Price Fluctuation

Our stock is thinly traded, so you may be unable to sell at or near ask prices or at all.

Our common stock trades on the OTCQB. Shares of our common stock are thinly-traded, meaning that the number of persons interested in purchasing our common shares at or near ask prices at any given time may be relatively small or non-existent. This situation is attributable to a number of factors, including:

●	we are a small company that is relatively unknown to stock analysts, stock brokers, institutional investors and others in the investment community that generate or influence sales volume; and

●	stock analysts, stock brokers and institutional investors may be risk-averse and be reluctant to follow an unproven, early stage company such as ours or purchase or recommend the purchase of our shares until such time as we became more seasoned and viable.

As a consequence, our stock price may not reflect an actual or perceived value. Also, there may be periods of several days or more when trading activity in our shares is minimal or non-existent, as compared to a seasoned issuer that has a large and steady volume of trading activity that will generally support continuous sales without an adverse effect on share price. A broader or more active public trading market for our common shares may not develop or if developed, may not be sustained. Due to these conditions, you may not be able to sell your shares at or near ask prices or at all if you need money or otherwise desire to liquidate your shares.

Even if an active trading market develops, the market price for our common stock may be highly volatile and could be subject to wide fluctuations.

We believe that newer alternative energy companies and companies that effect reverse mergers, such as our company, are particularly susceptible to speculative trading that may not be based on the actual performance of the company, which increases the risk of price volatility in a common stock. In addition, the price of the shares of our common stock could decline significantly if our future operating results fail to meet or exceed the expectations of market analysts and investors. Some of the factors that could affect the volatility of our share price include:

●	significant sales of our common stock or other securities in the open market;

●	speculation in the press or investment community;

●	actual or anticipated variations in quarterly operating results;

●	changes in earnings estimates;

●	publication (or lack of publication) of research reports about us;

●	increases in market interest rates, which may increase our cost of capital;

●	changes in applicable laws or regulations, court rulings and other legal actions;

●	changes in market valuations of similar companies;

●	additions or departures of key personnel;

●	actions by our stockholders; and

●	general market and economic conditions.

Trading in our common stock is subject to special sales practices and may be difficult to sell.

Our common stock is subject to the Securities and Exchange Commission’s “penny stock” rule, which imposes special sales practice requirements upon broker-dealers who sell such securities to persons other than established customers or accredited investors. Penny stocks are generally defined to be an equity security that has a market price of less than $5.00 per share. For purposes of the rule, the phrase “accredited investors” means, in general terms, institutions with assets in excess of $5,000,000, or individuals having a net worth in excess of $1,000,000 or having an annual income that exceeds $200,000 (or that, when combined with a spouse’s income, exceeds $300,000). For transactions covered by the rule, the broker-dealer must make a special suitability determination for the purchaser and receive the purchaser’s written agreement to the transaction prior to the sale. Consequently, the rule may affect the ability of broker-dealers to sell our securities and also may affect the ability of our shareholders in this offering to sell their securities in any market that might develop.

Stockholders should be aware that, according to Securities and Exchange Commission Release No. 34-29093, the market for penny stocks has suffered from patterns of fraud and abuse. Such patterns include:

●	control of the market for the security by one or a few broker-dealers that are often related to the promoter or issuer;

●	manipulation of prices through prearranged matching of purchases and sales and false and misleading press releases;

●	“boiler room” practices involving high-pressure sales tactics and unrealistic price projections by inexperienced sales persons;

●	excessive and undisclosed bid-ask differentials and markups by selling broker-dealers; and

●	the wholesale dumping of the same securities by promoters and broker-dealers after prices have been manipulated to a desired level, along with the resulting inevitable collapse of those prices and with consequent investor losses.

Our management is aware of the abuses that have occurred historically in the penny stock market. Although we do not expect to be in a position to dictate the behavior of the market or of broker-dealers who participate in the market, management will strive within the confines of practical limitations to prevent the described patterns from being established with respect to our common stock.

Substantial future sales of our common stock shares in the public market could cause our stock price to fall.

If our stockholders sell substantial amounts of our common stock, or the public market perceives that stockholders might sell substantial amounts of our common stock, the market price of our common stock could decline significantly. Such sales also might make it more difficult for us to sell equity or equity-related securities in the future at a time and price that our management deems appropriate. As of December 31, 2011, we had 69,760,667 shares of our common stock outstanding. We also have outstanding convertible notes (including accrued interest) with warrants convertible into approximately 46 million shares of our common stock, 4,000,000 shares of our common stock in escrow to be released upon future conditions and requirements and warrants, immediately exercisable and representing the right to purchase 2,300,000 shares of our common stock. An additional 14,000,000 shares of our common stock have been reserved for issuance pursuant to our 2007 Stock Option Plan.

Potential issuance of additional common and preferred stock could dilute existing stockholders.

We are authorized to issue up to 240,000,000 shares of common stock. To the extent of such authorization, our board of directors has the ability, without seeking stockholder approval, to issue additional shares of common stock in the future for such consideration as the board of directors may consider sufficient. We are also authorized to issue up to ten million shares of preferred stock, the rights and preferences of which may be designated in series by the board of directors. Such designation of new series of preferred stock may be made without stockholder approval, and could create additional securities which would have dividend and liquidation preferences over the common stock offered hereby. Preferred stockholders could adversely affect the rights of holders of common stock by:

●	exercising voting, redemption and conversion rights to the detriment of the holders of common stock;

●	receiving preferences over the holders of common stock regarding a surplus of funds in the event of our dissolution or liquidation;

●	delaying, deferring or preventing a change in control of our company; and

●	discouraging bids for our common stock.

Additionally, some of our convertible securities and warrants to purchase common stock have anti-dilution protection. This means that if we issue securities for a price less than the price at which these securities are convertible or exercisable for shares of common stock, the securities will become eligible to acquire more shares of common stock at a lower price, which will dilute the ownership of our common stockholders.

Finally, we have filed a registration statement pursuant to a registration rights agreement with some of our stockholders. The registration rights agreement provides, among other things, that we keep the registration statement associated with those shares continuously effective. If we are unable to comply with these provisions of the registration rights agreements, we may be obligated to pay those stockholders liquidated damages in the form of warrants to purchase additional common stock.

In all the situations described above, the issuance of additional common stock in the future will reduce the proportionate ownership and voting power of our current stockholders.

ITEM 1B. UNRESOLVED STAFF COMMENTS

Not applicable.

ITEM 2. PROPERTIES

We currently occupy 1,800 square feet of office space in St. Louis, Missouri. The lease has expired and we are in the process of renewing the lease while we continue to occupy the space. The monthly lease payment is $1,800, plus utilities. We took possession of the leased space in January, 2008.

ITEM 3. LEGAL PROCEEDINGS

Steve Vande Vegte v. various individuals and companies, including Cleantech Biofuels, Inc . - On September 22, 2010, we notified Bio-Products International, Inc. (“Bio-Products”) that it was in breach of the license agreement governing our license of the PSC technology to Bio-Products (a wholly-owned subsidiary of CES). We received a response from Bio-Products on November 5, 2010 disputing our claims. In February 2011, we became aware that Bio-Products effected a transfer of the license in violation of the license agreement. As a result, on March 21, 2011, we sent a notice of termination to Bio-Products and the transferee terminating the license agreement. In June 2011, Steve Vande Vegte, a shareholder in CES, filed a lawsuit against various individuals and companies, including the Company. The only Cause of Action against the Company is for Declaratory Relief seeking to avoid our March 2011 termination of the license to which Mr. Vande Vegte is not a party. On August 5, 2011, the Company filed a demurrer requesting that the court dismiss the case on the grounds that Mr. Vande Vegte lacks standing to pursue a claim concerning the license and that the claim raised in the complaint is not ripe. On December 8, 2011, the demurrer to dismiss Cleantech was granted. In October 2011, a Cross-Complaint was filed by Clean Conversion Technologies, Inc. (“CCT”) and Michael Failla v. Cleantech Biofuels, Inc. CCT is asking that the Company’s termination of the sub-license agreement is void. We intend to vigorously defend our rights.

Clean Conversion Technologies, Inc. v. Cleantech Biofuels, Inc . and Steve Vande Vegte - On January 30, 2012, CCT filed an anti-trust lawsuit against the defendants alleging monopolistic and anti-competitive acts to conspire to completely eliminate competition in an emerging line of commerce known as PSC conversion, which is a patented process owned by Cleantech (the PSC technology). On March 26, 2012, the Company filed a motion to dismiss. The hearing is currently set for May 7, 2012. We intend to vigorously defend our rights.

ITEM 4. (REMOVED AND RESERVED)

PART II

ITEM 5. MARKET FOR REGISTRANT’S COMMON EQUITY, RELATED STOCKHOLDER MATTERS AND ISSUER PURCHASES OF EQUITY SECURITIES

The following table sets forth for the periods indicated the high and low bid prices per share of our common stock as quoted on the OTCBB or Pink Sheets, as appropriate (in February 2011, the market-makers in our common stock have completed their migration off of FINRA's BB (Bulletin Board) to OTC Markets Group. As a result, the Company is categorized and quotes can currently be found under the OTCQB tier):

	Price Range of Common Stock
Year Ended December 31, 2009	High		Low
First Quarter	$	0.28	$	0.02
Second Quarter	$	0.45	$	0.05
Third Quarter	$	0.15	$	0.10
Fourth Quarter	$	0.16	$	0.06

Year Ended December 31, 2010
First Quarter	$	0.15	$	0.05
Second Quarter	$	0.14	$	0.04
Third Quarter	$	0.08	$	0.01
Fourth Quarter	$	0.06	$	0.03

Year Ended December 31, 2011
First Quarter	$	0.09	$	0.03
Second Quarter	$	0.07	$	0.04
Third Quarter	$	0.07	$	0.01
Fourth Quarter	$	0.06	$	0.01

On March 21, 2012, the closing price of our common stock, as quoted on the OTCQB, was $0.03 per share. As of March 21, 2012, we had approximately 130 stockholders of record.

In connection with the merger with SRS Energy, we assumed SRS Energy’s 2007 Stock Option Plan, which was adopted by the SRS Energy Board of Directors on April 16, 2007 and approved by the SRS Energy shareholders on April 16, 2007.

Equity Compensation Plan Information

Plan Category	Number of securities to be issued upon Exercise of Outstanding Options, Warrants and Rights		Weighted-Avg Exercise Price of Outstanding Options, Warrants and Rights		Number of Securities Remaining Available for Future Issuance Under Equity Compensation Plans (excluding securities reflected in column (a))
	(a)		(b)		(c)
Equity compensation plans approved by security holders: 2007 Stock Option Plan		11,292,000	$	0.11		2,708,000

Equity compensation plans not approved by security holders		-		-		-

Totals		11,292,000				2,708,000

Dividend Policy

We have no material operating history and therefore have had no earnings to distribute to stockholders. Even though we have recommenced operations, we do not anticipate paying any cash dividends in the foreseeable future. Rather, we currently intend to retain our earnings, if any, and reinvest them in the development of our business. Any future determination to pay cash dividends will be at the discretion of our board of directors and will be dependent upon our financial condition, results of operations, capital requirements, restrictions under any existing indebtedness and other factors the board of directors may deem relevant.

Recent Sales of Unregistered Securities –

During April 2009, the Company commenced a second offering of units comprised of a convertible promissory note and a warrant (this offering closed in September 2010). The Company raised a total of $1,198,500 of investment proceeds. Each convertible promissory note carries a one-year term and a 6% interest rate. In addition, each note can be converted into shares of the Company’s common stock, par value $0.001 per share (the “Common Stock”), at $0.08 per share at the holder’s option. Each note was issued with a warrant to purchase additional shares of Common Stock to provide 100% coverage of the principal amount of the associated note at a price of $0.30 per share. Two notes have been converted and beginning in March 2011, certain notes were exchanged into our November 2010 Offering as described below. As a result, as of December 31, 2011, we had $279,738 face value of notes outstanding. The issuance of units and the issuance of Common Stock upon conversion of notes were exempt from the registration requirements of the Securities Act of 1933, as amended (the “Securities Act”), pursuant to Rule 506 of Regulation D promulgated under the Securities Act (“Rule 506”) and/or Section 4(2) of the Securities Act.

During June 2010, the Company commenced another offering of units comprised of a convertible promissory note and a warrant. As of December 31, 2011, the Company had raised a total of $75,000 of investment proceeds. The convertible promissory note carried a one-year term, a 12% interest rate and a payback provision of the note if $250,000 or more in the aggregate is raised by the Company in future offerings. In addition, the note could have been converted, at the note holder’s option, at any time during the one-year term into shares of Common Stock at $0.08 per share, or prior to the closing of any Qualifying Equity Financing (minimum capital received of $5 million). Each note was issued with a warrant to purchase additional shares of Common Stock to provide for 100% coverage of the promissory note at a price of $0.30 per share. Upon maturity in June 2011, this note was exchanged into our November 2010 Offering as described below. As a result, the balance due on this offering is $-0-.The issuance of units and the issuance of Common Stock upon conversion of notes were exempt from the registration requirements of the Securities Act, pursuant to Rule 506 and/or Section 4(2) of the Securities Act.

In September 2010, the Company issued a note in the amount of $100,000 (interest at 6.0% per annum through May 15, 2011 and 10.0% thereafter and secured by a security interest in the PSC Patent) and issued warrants to purchase 2,000,000 shares of Common Stock at a price of $0.05 per share. The note is due the earlier of: (i) May 15, 2012 (extended from February 28, 2011 through various amendments) or (ii) the date on which $500,000 or more in the aggregate is raised by the Company in future offerings. The warrants are exercisable at any time for five years from the date of issuance or reissuance (the warrants were re-dated November 7, 2011 with an amendment). The issuance of Common Stock upon conversion of warrants was exempt from the registration requirements of the Securities Act, pursuant to Rule 506 and/or Section 4(2) of the Securities Act.

During November 2010, the Company commenced a third offering of units comprised of a convertible promissory note and a warrant. As of December 31, 2011, the Company raised a total of $400,000 of investment proceeds. Each convertible promissory note carries a one-year term and a 6% interest rate. In addition, each note can be converted into shares of Common Stock at $0.06 per share at the holder’s option. Each note was issued with a warrant to purchase additional shares of Common Stock to provide 100% coverage of the principal amount of the associated note at a price of $0.30 per share. Three notes were converted during 2011. As of December 31, 2011, we had $1,884,865 face value of notes outstanding, which includes the exchanged notes from our April 2009 and June 2010 Offerings. The issuance of units and the issuance of Common Stock upon conversion of notes were exempt from the registration requirements of the Securities Act, pursuant to Rule 506 and/or Section 4(2) of the Securities Act.

In July 2011, 333,333 restricted shares of the Company’s common stock were issued to a consultant in exchange for $20,000 owed to the consultant for consulting fees. The issuance of the common stock was exempt from the registration requirements of the Securities Act, pursuant to Rule 506 and/or Section 4(2) of the Securities Act.

In August 2011, an aggregate 600,000 restricted shares of the Company’s common stock were issued, in equal shares, to our non-management directors in recognition of their additional service and assistance to the Company outside of their duties as a member of the Company’s Board of Directors. The issuance of the common stock was exempt from the registration requirements of the Securities Act, pursuant to Rule 506 and/or Section 4(2) of the Securities Act.

In September 2011, 200,000 restricted shares of the Company’s common stock were issued to a former employee as part of a final settlement agreement. The issuance of the common stock was exempt from the registration requirements of the Securities Act, pursuant to Rule 506 and/or Section 4(2) of the Securities Act.

ITEM 6. SELECTED FINANCIAL DATA

Not applicable.

ITEM 7. MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS

The following discussion of our plan of operation should be read in conjunction with the financial statements and related notes to the financial statements included elsewhere in this report. This discussion contains forward-looking statements that relate to future events or our future financial performance. These statements involve known and unknown risks, uncertainties and other factors that may cause our actual results, levels of activity or performance to be materially different from any future results, levels of activity or performance. These risks and other factors include, among others, those listed under “Statement Regarding Forward-Looking Statements” and “Risk Factors” and those included elsewhere in this report.

Plan of Operation

Biomass Feedstock Production

Bio-Fuel and Bio-Chemical Joint Testing/Research

New Technologies; Commercializing Existing Technologies

To commercialize our technology, we intend to:

●	construct and operate a commercial plant that: (i) processes MSW into cellulosic biomass for conversion into energy or chemical products and (ii) separates recyclables (metals, plastics, glass) for single-stream recycling;

●	identify and partner with landfill owners, waste haulers and municipalities to identify locations suitable for our technology; and

●	pursue additional opportunities to implement our technology in commercial settings at transfer stations and landfills in the United States and elsewhere in the world.

As a result of the limited operating history of our company, prior years’ financial statements provide little information and virtually no guidance as to our future performance. In order to finance our business beyond this stage, we will be required to raise additional capital. Management plans to secure additional funds through through future sales of the Company’s Common Stock, government grants, project financings, preferred stock or debentures, until such time as the Company’s revenues and cash flow are sufficient to meet its cost structure and ultimately achieve profitable operations. The consolidated financial statements do not include any adjustments that might result from the outcome of these uncertainties. We may not be able to secure financing on favorable terms, or at all. If we are unable to obtain acceptable financing on a timely basis, our business will likely fail and our common stock may become worthless.

Results of Operations

The following tables set forth the amounts of expenses and changes in our consolidated statements of operations:

Year ended December 31, 2011 compared to the year ended December 31, 2010

	Years ended December 31,
	2011			2010			Change			% Change
Costs and expenses:
General and administrative	$	466,710		$	691,428		$	(224,718	)		-33	%
Professional fees		125,866			91,227			34,639			38	%
		592,576			782,655			(190,079	)

Other expense (income):
Interest		176,565			407,197			(230,632	)		-57	%
Other income		(50,000	)		-			(50,000	)		N/M
Interest income		1,572			(8,219	)		9,791			-119	%

Net loss applicable to common stockholders	$	720,713		$	1,181,633		$	(460,920	)		-39	%

Costs and expenses:

General and administrative – The decrease in 2011 is due primarily to a decrease in salaries and share-based compensation of approximately $160,000 and a decrease of approximately $60,000 in marketing expenses.

Professional Fees – The increase in 2011 is due primarily to increases in consulting fees.

Other expense (income):

Interest expense – The decrease in 2011 is due to decreased amortization of approximately $245,000 of discounts related to various notes as the remaining discounts became fully amortized during 2011, offset by an increase of $15,000 in interest expense on our convertible notes due to the addition of new notes in 2011.

Other income – Included in 2011 is $50,000 related to a diesel fuel production agreement not completed.

Interest income – Included in 2011 is approximately $15,000 to write-off accrued interest related to Notes issued for restricted stock grants that expired and were not paid.

Year ended December 31, 2010 compared to the year ended December 31, 2009

	Years ended December 31,
	2010			2009			Change			% Change
Costs and expenses:
General and administrative	$	691,428		$	1,087,889		$	(396,461	)		-36	%
Professional fees		91,227			290,023			(198,796	)		-69	%
Research and development		-			693,146			(693,146	)		-100	%
		782,655			2,071,058			(1,288,403	)

Other expense (income):
Interest		407,197			906,535			(499,338	)		-55	%
Other income		-			(32,000	)		32,000			N/M
Interest income		(8,219	)		(11,771	)		3,552			-30	%

Net loss applicable to common stockholders	$	1,181,633		$	2,933,822		$	(1,752,189	)		-60	%

Costs and expenses:

General and administrative – The decrease in 2010 is due primarily to a decrease in salaries and share-based compensation of approximately $330,000 and a decrease of approximately $70,000 in marketing expenses.

Professional Fees – The decrease in 2010 is due to reductions in legal and consulting fees of approximately $132,000 and $65,000, respectively.

Research and Development – The expense in 2009 is entirely related to the write-off of our license asset related to the HFTA technology as we elected to terminate the license agreement during the fourth quarter of 2009. As we shifted our plan of operation from a fully-integrated producer of cellulosic ethanol to the commercialization of our technology for cleaning and separating MSW into its component parts as described earlier in this report, we have had no R&D expense in 2010.

Other expense (income):

Interest expense – The decrease in 2010 is due primarily to decreased amortization of approximately $500,000 of discounts related to various notes as the majority of these discounts became fully amortized during 2010.

Other income – The other income in 2009 was for a two-month lease and subsequent sale of the HFTA equipment previously purchased.

Liquidity and Capital Resources

As a development-stage company, we have no revenues and will be required to raise additional capital in order to execute our business plan and commercialize our products. Beginning in September 2008 and as of March 23, 2012, we raised an aggregate of $2.5 million, in separate offerings of units comprised of a convertible note and warrants. We are continuing to explore opportunities to raise cash through the issuance of these units and other financing opportunities. As of March 23, 2012, our current cash is not sufficient to fund our operations. Our liabilities are substantially greater than our current available funds. We are seeking additional financing through the sale of additional equity, various government funding opportunities and/or possibly through strategic alliances with larger energy or waste management companies. We have terminated our agreement with Houlihan Capital but the Company is continuing to explore and evaluate a range of strategic financing alternatives and/or other transactions. However, we may not be successful in securing additional capital. If we are not able to obtain additional financing in the immediate future, we will be required to delay our development until such financing becomes available. Further, even assuming that we secure additional funds, we may never achieve profitability or positive cash flow. If we are not able to timely and successfully raise additional capital and/or achieve profitability or positive cash flow, we will not have sufficient capital resources to implement our business plan.

Debt

Convertible Notes Payable

Since September 2008, the Company has conducted four offerings of units comprised of a one-year convertible promissory note and a warrant having the terms set forth below:

Offering	Note Interest Rate			Note Conversion Price		Warrant Exercise Price		Closed or Open
2008 Offering		6.0	%	$	0.25	$	0.45	Closed
2009 Offering		6.0	%	$	0.08	$	0.30	Closed
6/10 Offering		12.0	%	$	0.08	$	0.30	Closed
11/10 Offering		6.0	%	$	0.06	$	0.30	Open

Each note may be converted, at the note holder’s option, at any time during the one-year term of the note or prior to the closing of any “Qualifying Equity Financing (minimum capital received of $5 million) into shares of Common Stock at the conversion price noted above. All notes have been recorded as short-term debt (notes payable) in the financial statements, net of discounts for the conversion and warrant features (except for the 11/10 Offering which carried no discounts). The discounts have been amortized on a straight-line basis over the term of each note and are fully amortized as of December 31, 2011. Amortization of the discounts (included in interest expense in the financial statements) is as follows:

	2011		2010		2009
2008 Offering	$	-	$	7,137	$	523,791
2009 Offering		26,596		253,481		113,344
6/10 Offering		11,573		13,571		-
CMS Acquisition, LLC		3,492		7,222		-
Vertex		-		6,558		178,392
Total amortization	$	41,661	$	287,969	$	815,527

2008 Offering - During September 2008, the Company commenced an offering of units and raised a total of $642,000 of investment proceeds through March 31, 2009. As of March 31, 2010, all of these notes had either been converted to shares of our common stock or exchanged into our 2009 Offering (resulting in new notes with a total face value of $539,829, which included the original principal and interest through the date of exchange).

2009 Offering - During April 2009, the Company commenced an offering of units and raised a total of $1,198,500 of investment proceeds through August 2010. One note was converted to shares of Common Stock during the second quarter of 2009 and one note was converted to shares of Common Stock during the second quarter 2010. Beginning in March 2011, certain notes were exchanged into our 11/10 Offering. As a result, as of December 31, 2011, we had $279,738 face value of notes outstanding, which includes the exchanged notes from our 2008 Offering. The first of these notes matured in April 2010. We are working with the remaining noteholders to either: repay the notes, refinance to our 11/10 Offering or convert the notes to shares of our Common Stock.

6/10 Offering - During June 2010, the Company commenced an offering of units and raised a total of $75,000 of investment proceeds in one note. Upon maturity in June 2011, this note was exchanged into our 11/10 Offering. As a result, the balance due on this offering is $-0-.

11/10 Offering - During November 2010, the Company commenced an offering of units, and as of December 31, 2011, had raised a total of $400,000 of investment proceeds. Two notes were converted during the first quarter of 2011 and one during the fourth quarter of 2011. As of December 31, 2011, we had $1,884,865 face value of notes outstanding, which includes the exchanged notes from our 2009 Offering.

CMS Acquisition, LLC Note Payable

In September 2010, the Company issued a note in the amount of $100,000 (interest at 6.0% per annum through May 15, 2011 and 10.0% thereafter and secured by a security interest in the PSC Patent) and issued warrants to purchase 2,000,000 shares of Common Stock at a price of $0.05 per share. The note is due the earlier of: (i) May 15, 2012 (extended from February 28, 2011 through various amendments) or (ii) the date on which $500,000 or more in the aggregate is raised by the Company in future offerings. The warrants are exercisable at any time for five years from the date of issuance or reissuance (the warrants were re-dated November 7, 2011 with an amendment). The value of these warrants has been recorded as a contra-balance amount discount with the note and was amortized (interest expense) through the original due date of February 28, 2011.

Summary of Cash Flow Activity

	For the Years Ended December 31,
	2011			2010			2009
Net cash used by operating activities	$	(280,510	)	$	(245,033	)	$	(715,264	)
Net cash used by investing activities		-			-			(20,702	)
Net cash provided by financing activities		274,537			250,094			640,261

Net cash used by operating activities

During 2011 and 2010, cash used by operating activities was impacted primarily by increases in accounts payable and other accrued liabilities.

Net cash used by investing activities

During 2009, cash used by investing activities was for capital expenditures.

Net cash provided by financing activities

During 2011, 2010 and 2009, cash provided by financing activities was primarily from the continued issuance of our Convertible Notes for $365,000, $485,000 and $958,500, respectively, offset by payments against other Notes Payable.

Contractual Obligations and Commitments

In the table below, we set forth our obligations as of December 31, 2011. Some of the figures we include in this table are based on our estimates and assumptions about these obligations, including their durations, anticipated actions by third parties and other factors. The obligations we may pay in future periods may vary from those reflected in this table because of estimates or actions of third parties as disclosed in the notes to the table.

	Payments due by Period
	Total		Less than 1 year		1 to 3 years		4 to 5 years		More than 5 years
Convertible Notes (1)	$	2,264,000	$	2,264,000	$	-	$	-	$	-
CMS Acquition Note (2)		84,000		84,000		-		-		-
Operating Lease (3)		-		-		-		-		-
Total contractual obligations	$	2,348,000	$	2,348,000	$	-	$	-	$	-

(1)

Amount represents value of principal amount of notes and estimates for interest. These notes are with various individuals, carry one-year terms and are convertible into shares of Common Stock at the noteholders option. The first of these notes matured in April 2010. We are working with the noteholders to refinance their notes, convert their notes into shares of Common Stock or repay the notes.

(2)	Amount represents value of principal amount of note and interest and is secured by a security interest in the PSC Patent. Final payment on this note is due May 15, 2012.

(3)	The lease for our office space has expired and we are currently working on a new lease while we occupy the space.

Off-Balance Sheet Arrangements

We have no off-balance sheet arrangements.

We have not entered into any transaction, agreement or other contractual arrangement with an unconsolidated entity under which we have:

●	a retained or contingent interest in assets transferred to the unconsolidated entity or similar arrangement that serves as credit;

●	liquidity or market risk support to such entity for such assets; or

●

an obligation, including a contingent obligation, arising out of a variable interest in an unconsolidated entity that is held by, and material to, us where such entity provides financing, liquidity, market risk or credit risk support to, or engages in leasing, hedging, or research and development services with us.

Critical Accounting Estimates

Long-Lived Assets – Our acquisition and merger activities have resulted in aggregate licensing and patent assets of approximately $2.1 million as of December 31, 2011. We are required to conduct impairment tests of long-lived assets on an annual basis and between annual tests if an event occurs or circumstances change that would more likely than not reduce the fair value of an asset below its carrying value. As we have not commenced commercial operations, these assets have not yet been placed in service.

Deferred Taxes - We recognize deferred income tax liabilities and assets for the expected future tax consequences of events that have been recognized in the financial statements or tax returns. Under this method, deferred tax liabilities and assets are determined based on the differences between the financial statement carrying amounts and the tax basis of assets and liabilities using enacted tax rates in effect in the years in which the differences are expected to reverse. The Company incurred no income taxes to date. Any benefits are the result of temporary differences (start-up costs, stock compensation and other items) and operating loss carryforwards. The difference between the expected income tax benefit and non-recognition of an income tax benefit in each period is the result of a valuation allowance applied to deferred tax assets. A valuation allowance in the same amount of the benefit has been provided to reduce the deferred tax asset, as realization of the asset is not assured.

Stock-Based Compensation - We account for stock-based compensation in accordance with accounting guidance that requires measuring all stock-based compensation awards at fair value and recognizing an expense in the financial statements. We compensate certain employees, officers, directors and consultants with share-based payment awards and recognize compensation costs for these awards based on their fair values and expense is recognized over the requisite service period. The fair values of certain awards are estimated on the grant date using the Black-Scholes-Merton option-pricing formula, which incorporates certain assumptions including the expected term of an award and expected stock price volatility.

Convertible Notes Payable and Warrants – The Company has issued Convertible Promissory Notes (“Notes”). These Notes may be converted at the option of the noteholder into shares of the Company’s common stock. Additionally, these Notes carry warrants for shares of the Company’s common stock. These promissory notes have been recorded as short-term debt (notes payable) in the financial statements, net of discounts for the conversion and warrant features. The discounts have been amortized on a straight-line basis over the term of each note.

Fair Value Measurement - We use fair value accounting and reporting to specify a hierarchy of valuation techniques based upon whether the inputs to those valuation techniques reflect assumptions other market participants would use based upon market data obtained from independent sources or reflect our own assumptions of market participant valuation. The hierarchy is broken down into three levels based on the reliability of the inputs as follows:

●	Level 1 – Quoted prices in active markets that are unadjusted and accessible at the measurement date for identical, unrestricted assets or liabilities;

●	Level 2 – Quoted prices for identical assets and liabilities in markets that are not active, quoted prices for similar assets and liabilities in active markets, or financial instruments for which significant inputs are observable, either directly or indirectly;

●	Level 3 – Prices or valuations that require inputs that are both significant to the fair value measurement and unobservable.

As of and during the year ended December 31, 2011 and 2010, we utilized Level 1 inputs to determine the fair value of cash equivalents and we utilized Level 2 inputs to determine the fair value of certain long-lived assets.

Contingent Liabilities – We are, from time to time, subject to litigation to our business. Assessments regarding the ultimate cost of lawsuits require judgments concerning matters such as the anticipated outcome of negotiations, the number and cost of pending and future claims, and the impact of evidentiary requirements. A significant amount of judgment and use of estimates is required to quantify our ultimate exposure in these matters. We regularly review the valuation of these liabilities and account for changes in circumstances for ongoing and emerging issues. The Company intends to defend itself vigorously in all litigation.

ITEM 7A. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

As of December 31, 2011, all of our debt instruments (Notes Payable) carry fixed interest rates. We do not have any arrangements for borrowings under a credit facility. We currently have no operations and are not subject to any currency fluctuations or credit risk.

ITEM 8. FINANCIAL STATEMENTS AND SUPPLEMENTAL DATA

REPORT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM

To the Board of Directors and Stockholders of

CleanTech Biofuels, Inc.

St. Louis, Missouri

We have audited the accompanying consolidated balance sheets of CleanTech Biofuels, Inc. (a development stage company) and subsidiaries as of December 31, 2011, 2010 and 2009, and the related consolidated statements of operations, changes in stockholders’ equity, and cash flows for each of the years in the three-year period ended December 31, 2011 and for the period from July 14, 2004 (inception) to December 31, 2011. CleanTech Biofuels Inc.’s management is responsible for these consolidated financial statements. Our responsibility is to express an opinion on these consolidated financial statements based on our audits.

We conducted our audits in accordance with the standards of the Public Company Accounting Oversight Board (United States). Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the consolidated financial statements are free of material misstatement. The Company and its subsidiaries are not required to have, nor were we engaged to perform, an audit of their internal control over financial reporting. Our audit included consideration of internal control over financial reporting as a basis for designing audit procedures that are appropriate in the circumstances, but not for the purpose of expressing an opinion on the effectiveness of the Company’s internal control over financial reporting. Accordingly, we express no such opinion. An audit also includes examining, on a test basis, evidence supporting the amounts and disclosures in the consolidated financial statements, assessing the accounting principles used and significant estimates made by management, as well as evaluating the overall financial statement presentation. We believe that our audits provide a reasonable basis for our opinion.

In our opinion, the consolidated financial statements referred to above present fairly, in all material respects, the financial position of CleanTech Biofuels, Inc. and subsidiaries as of December 31, 2011, 2010 and 2009, and the results of their operations and their cash flows for the years in the three-year period ended December 31, 2011 and from July 14, 2004 (inception) to December 31, 2011, in conformity with accounting principles generally accepted in the United States of America.

The accompanying consolidated financial statements have been prepared assuming that the Company and its subsidiaries will continue as a going concern. As discussed in Note 1 to the financial statements, the Company’s significant operating losses and recent inability to secure additional capital to implement its business plan raise substantial doubt about its ability to continue as a going concern. The consolidated financial statements do not include any adjustments that might result from the outcome of this uncertainty.

MILHOUSE & NEAL, LLP

Certified Public Accountants

March 6, 2012

CLEANTECH BIOFUELS, INC.

(formerly Alternative Ethanol Technologies, Inc.)

(A Development Stage Company)

CONSOLIDATED BALANCE SHEETS

	December 31,			December 31,
	2011			2010
ASSETS
Current Assets:
Cash and cash equivalents	$	-		$	5,973
Prepaids and other current assets		41,599			39,905
		41,599			45,878

Property and equipment, net		4,783			9,777

Non-Current Assets:
Technology license		1,521,250			1,521,250
Patents		600,000			600,000
Total Assets	$	2,167,632		$	2,176,905

LIABILITIES AND STOCKHOLDERS' EQUITY (DEFICIT)
Current Liabilities:
Accounts payable	$	370,410		$	392,950
Accrued interest		105,009			121,260
Accrued professional fees and other		716,427			487,835
Notes payable, net		2,242,299			1,871,669
Deferred revenue		-			50,000
Capital lease		-			1,211
Total Current Liabilities		3,434,145			2,924,925

STOCKHOLDERS' EQUITY (DEFICIT)
Preferred stock, $0.001 par value; 10,000,000 authorized shares; no shares
issued or outstanding		-			-
Common stock, $0.001 par value; 240,000,000 authorized shares;
69,760,667 and 68,309,679 shares issued and outstanding at
December 31, 2011 and 2010, respectively		69,761			68,310
Additional paid-in capital		6,366,823			6,301,726
Notes receivable - restricted common stock		(159,385	)		(295,057	)
Deficit accumulated during the development stage		(7,543,712	)		(6,822,999	)
Total Stockholders' Equity (Deficit)		(1,266,513	)		(748,020	)
Total Liabilities and Stockholders' Equity (Deficit)	$	2,167,632		$	2,176,905

The accompanying notes are an integral part of these financial statements

CLEANTECH BIOFUELS, INC.

(formerly Alternative Ethanol Technologies, Inc.)

(A Development Stage Company)

CONSOLIDATED STATEMENTS OF OPERATIONS

										July 14, 2004
										(inception) to
	Years ended December 31,									December 31,
	2011			2010			2009			2011
Costs and expenses:
General and administrative	$	466,710		$	691,428		$	1,087,889		$	3,313,777
Professional fees		125,866			91,227			290,023			1,266,557
Research and development		-			-			693,146			1,217,847
		592,576			782,655			2,071,058			5,798,181

Other expense (income):
Interest		176,565			407,197			906,535			1,736,755
Amortization of technology license		-			-			-			35,000
Deposit forfeiture		-			-			-			(25,000	)
Other income		(50,000	)		-			(32,000	)		(82,000	)
Interest income		1,572			(8,219	)		(11,771	)		(53,572	)
		128,137			398,978			862,764			1,611,183

Income tax benefit		-			-			-			-

Net loss	$	720,713		$	1,181,633		$	2,933,822		$	7,409,364


Basic and diluted net loss per common share	$	0.01		$	0.02		$	0.05		$	0.14
Weighted average common shares outstanding		69,104,910			67,924,219			63,069,675			53,192,754

The accompanying notes are an integral part of these financial statements

CLEANTECH BIOFUELS, INC.

(formerly Alternative Ethanol Technologies, Inc.)

(A Development Stage Company)

Consolidated Statements of Changes in Stockholders' Equity (Deficit)

										Notes Rec -
							Additional			restricted			July 14, 2004
	Common Stock						Paid-in			common			(inception) to
	Shares			Amount			Capital			stock			Dec 31, 2011
Balances at December 31, 2008		61,270,153		$	61,270		$	4,675,098		$	(162,567	)	$	(2,707,544	)
Conversions of convertible notes in 2009 at $.25 per share		466,268			466			116,102
Conversions of convertible notes in 2009 at $.08 per share		687,500			688			35,967
Discounts on Notes Payable								391,069
Issuances of shares in August 2009 at $.13 per share for
Net Issuance Elections for warrants		357,778			358			(358	)
Issuance of restricted shares in June and December 2009
at $.12 and $.06 per share, respectively		1,250,000			1,250			111,250			(112,500	)
Shares released from escrow to HFTA in Aug-09 at $.10/share		1,925,125			1,925			190,587
Issuance of restricted shares to Directors in Sep-09 at
$.10 per share		300,000			300			29,700			(30,000	)
Interest on Notes Receivable											(11,771	)
Stock-based compensation								361,721
Net loss														(2,933,822	)
Balances at December 31, 2009		66,256,824			66,257			5,911,136			(316,838	)		(5,641,366	)
Discounts on Notes Payable								128,054
Issuance of restricted shares to a Director in Feb-10 at
$.10 per share		150,000			150			14,850			(15,000	)
Conversion of Debentures in Apr-10 at $.08 per share		2,069,375			2,069			163,480
Conversion of Convertible Note in June-10 at $0.08/share		133,480			134			10,545
Interest on Notes Receivable											(16,815	)
Expiration of Notes Receivable in Aug-10 at $0.15/share		(300,000	)		(300	)		(44,700	)		53,596
Stock-based compensation								118,361
Net loss														(1,181,633	)
Balances at December 31, 2010		68,309,679			68,310			6,301,726			(295,057	)		(6,822,999	)
Conversion of Convertible Notes in 2011 at $0.06/share		1,627,655			1,627			96,032			-			-
Expiration of Note Receivable in June-11 at $0.12/share		(625,000	)		(625	)		(74,375	)		82,514			-
Expiration of Note Receivable in Dec-11 at $0.06/share		(625,000	)		(625	)		(36,875	)		41,252			-
Expiration of Note Receivable in Dec-11 at $0.36/share		(60,000	)		(60	)		(21,540	)		24,995			-
Issuance of restricted shares to consultant in July-2011
at $0.06 per share		333,333			334			19,666			-			-
Issuance of restricted shares to directors in Aug-2011
at $0.055 per share		600,000			600			32,400			-			-
Issuance of restricted shares to former employee in
Sep-2011 at $0.05 per share		200,000			200			9,800			-			-
Interest on Notes Receivable		-			-			-			(13,089	)		-
Stock-based compensation		-			-			39,989			-			-
Net loss		-			-			-			-			(720,713	)
Balances at December 31, 2011		69,760,667		$	69,761		$	6,366,823		$	(159,385	)	$	(7,543,712	)

The accompanying notes are an integral part of these financial statements.

CLEANTECH BIOFUELS, INC.

(formerly Alternative Ethanol Technologies, Inc.)

(A Development Stage Company)

CONSOLIDATED STATEMENTS OF CASH FLOWS

										July 14, 2004
										(inception) to
	Year Ended December 31,									December 31,
Operating Activities	2011			2010			2009			2011
Net loss applicable to common stockholders	$	(720,713	)	$	(1,181,633	)	$	(2,933,822	)	$	(7,409,364	)
Adjustments to reconcile net loss applicable to common
stockholders to net cash used by operating activities:
Items that did not use (provide) cash:
Common stock issued for organizational costs		-			-			-			100
Depreciation		4,994			10,531			19,220			63,573
Amortization		-			-			-			35,000
Interest income		1,572			(8,219	)		(11,771	)		(26,185	)
Amortization of discounts (interest expense) and
other financing charges		41,662			287,968			815,526			1,284,106
Share-based compensation expense		39,989			118,361			361,721			778,192
Issuance of restricted common stock		63,000			-			-			63,000
Write-off of technology license		-			-			693,045			790,545
Fair value of RAM warrant settlement		-			-			-			125,027
Changes in operating assets and liabilities that provided
(used) cash, net:
Prepaids and other current assets		(194	)		7,191			53,440			(20,098	)
Technology license		-			-			-			(132,500	)
Accounts payable		(22,540	)		90,052			63,973			370,410
Other assets and other liabilities		83,128			118,574			113,961			391,302
Accrued liabilities		228,592			312,142			109,443			716,427
Net cash used by operating activities		(280,510	)		(245,033	)		(715,264	)		(2,970,465	)

Cash Flows Provided (Used) by Investing Activities
Acquisition of patent, net		-			-			-			(150,000	)
Merger of Biomass North America Licensing, Inc., net		-			-			-			(20,000	)
Acquisition of HFTA technology, net		-			-			-			-
Expenditures for equipment		-			-			(20,702	)		(54,237	)
Net cash used by investing activities		-			-			(20,702	)		(224,237	)

Cash Flows Provided (Used) by Financing Activities
Advances - related parties		(1,500	)		(10,615	)		(21,576	)		(21,500	)
Payments on capital lease, including interest		-			(4,959	)		(5,049	)		(13,903	)
Series A Convertible Debentures, including interest		-			-			-			1,424,900
Issuance of Note Payable		-			100,000			-			100,000
Issuance of Convertible Notes Payable		365,000			385,000			958,500			2,315,500
Payments on Notes Payable		(88,963	)		(219,332	)		(291,614	)		(635,295	)
Sale of common stock		-			-			-			25,000
Net cash provided by financing activities		274,537			250,094			640,261			3,194,702
Net increase (decrease) in cash and cash equivalents		(5,973	)		5,061			(95,705	)		-
Cash and cash equivalents at beginning of period		5,973			912			96,617			-
Cash and cash equivalents at end of period	$	-		$	5,973		$	912		$	-

The accompanying notes are an integral part of these financial statements

CLEANTECH BIOFUELS, INC.

(formerly Alternative Ethanol Technologies, Inc.)

(A Development Stage Company)

CONSOLIDATED STATEMENTS OF CASH FLOWS cont'd

							July 14, 2004
							(inception) to
	Year Ended December 31,						December 31,
	2011		2010		2009		2011

Supplemental disclosure of cash flow information:
Cash paid for interest	$	12,172	$	721	$	3,036	$	23,139

Supplemental disclosure of noncash investing and
financing activities:
Promissory notes receivable related to Series A Convertible Debentures	$	-	$	-	$	-	$	450,000
Capital lease related to the purchase of equipment	$	-	$	-	$	-	$	14,119
Common stock issued for organizational costs	$	-	$	-	$	-	$	100
Common stock issued to consultant, directors and former employee	$	63,000	$	-	$	-	$	63,000
Common stock issued for promissory notes	$	-	$	-	$	-	$	133,596
Common stock issued for Debentures converted	$	-	$	165,550	$	-	$	1,498,887
Common stock issued for convertible notes converted	$	97,659	$	10,678	$	153,009	$	280,429
Common stock and note payable issued for acquistion of Biomass	$	-	$	-	$	-	$	1,501,250
Common stock issued for HFTA	$	-	$	-	$	192,513	$	693,045

The accompanying notes are an integral part of these financial statements

CLEANTECH BIOFUELS, INC.

(A DEVELOPMENT STAGE COMPANY)

NOTES TO CONSOLIDATED FINANCIAL STATEMENTS

Note 1 – Organization and Business

Alternative Ethanol Technologies, Inc. (the “Company”), was incorporated in Delaware on December 20, 1996. Effective August 2, 2007, the Company changed its name to CleanTech Biofuels, Inc.

On March 27, 2007, the Company acquired SRS Energy, Inc., a Delaware corporation (“SRS Energy”), pursuant to an Agreement and Plan of Merger and Reorganization. In accordance with the merger agreement, SRS Acquisition Sub, Inc., a Delaware corporation and wholly-owned subsidiary of the Company, merged with and into SRS Energy. The merger was consummated on May 31, 2007 and resulted in SRS Energy becoming a wholly-owned subsidiary of the Company. As a result of the merger, the stockholders of SRS Energy surrendered all of their issued and outstanding common stock and received shares of the Company’s common stock, $.001 par value per share (“Common Stock”). The former parent of SRS Energy, Supercritical Recovery Systems, Inc., immediately prior to the merger, distributed 78.8% of its 96% ownership in SRS Energy to its shareholders on a pro rata basis.

For accounting purposes, because the Company had been a public shell company prior to the merger, the merger was treated as an acquisition of the Company and a recapitalization of SRS Energy. As a result, the historical information of the Company prior to the merger is that of SRS Energy. In addition, historical share amounts have been restated to reflect the effect of the merger.

The Company is a development stage company that has been engaged in technology development and pre-operational activities since its formation. The Company is currently in the process of raising capital to design and build a commercial biomass recovery plant to provide biomass feedstock for customer evaluation and trial purchases. Initially, the biomass feedstock output will be sold or provided to electric utilities, power and steam producers, and biofuel and chemical research firms for evaluation. In addition to research and development, the Company is also working towards licensing and/or developing potential commercial projects. These projects plan to focus on cleaning and separating municipal solid waste (also referred to as MSW) into its component parts in order to obtain: (i) a homogenous feedstock of cellulosic biomass for producing energy and other chemical products and (ii) recyclable products (metals, plastics, aluminum).

The Company has no operating history as a producer of biomass or energy sources and has not constructed any plants to date. We have no revenues and will be required to raise additional capital in order to execute our business plan and commercialize our products. Our current cash is not sufficient to fund our current operations. Our liabilities are substantially greater than our current available funds. Although we continue to seek additional financing through the sale of additional equity, various government funding opportunities and/or possibly through strategic alliances with larger energy or waste management companies, we have not had recent success securing meaningful amounts of financing. The Company will require substantial additional capital to implement its business plan and it may be unable to obtain the capital required to do so. If we are not able to immediately and successfully raise additional capital and/or achieve profitability or positive cash flow, we may not be able to continue operations.

Note 2 – Summary of Significant Accounting Policies

Use of Estimates - The preparation of financial statements in conformity with United States generally accepted accounting principles requires management to make estimates and assumptions that affect the amounts reported in the financial statements and accompanying notes. Management makes these estimates using the best information available at the time the estimates are made; however, actual results could differ materially from those estimates. Except where otherwise noted, the words “we,” “us,” “our,” and similar terms, as well as “Cleantech” or the “Company,” refer to Cleantech Biofuels, Inc. and its’ subsidiaries, collectively.

Consolidation - The financial statements include the accounts of Cleantech Biofuels, Inc. and its wholly owned subsidiaries, SRS Energy, Inc. and CTB Licensing, LLC. All significant intercompany transactions and balances are eliminated in consolidation.

Research and Development Costs - Research and development expenditures (which are comprised of costs incurred in performing research and development activities including wages and associated employee benefits, facilities and overhead costs), including payments to collaborative research partners are expensed as incurred.

Impairment of Long-Lived Assets - The Company continually evaluates whether events and circumstances have occurred that indicate the remaining estimated useful life of long-lived assets may warrant revision or that the remaining balance may not be recoverable primarily through reviewing changes in business plans and use of such assets. When factors indicate that an asset should be evaluated for possible impairment, the Company reviews long-lived assets to assess future use or recoverability of such asset. Impairments are recognized in earnings to the extent that the carrying value exceeds fair value. An impairment loss of approximately $690,000 was recorded in the year ended December 31, 2009. See further footnote disclosures for details of this impairment.

Intellectual Property - Intellectual property, consisting of our licensed/owned patents and other proprietary technology, are stated at cost and will be amortized on a straight-line basis over their economic estimated useful life. Costs and expenses incurred in creating intellectual property are expensed as incurred. The cost of purchased intellectual property is capitalized. Amortization of these assets has not yet begun as the assets have not been placed in service as we have not yet commenced operations.

Property, plant and equipment - Newly acquired property, plant and equipment are carried at cost less accumulated depreciation. Depreciation is provided over the estimated useful lives of the assets, on the straight-line method for financial reporting purposes. Expenditures for maintenance and repairs are charged to expense as incurred.

Income Taxes - The Company accounts for income taxes in accordance with accounting guidance, which requires the Company to provide a net deferred tax asset/liability equal to the expected future tax benefit/expense of temporary reporting differences between financial statement and tax accounting methods and any available operating loss or tax credit carry forwards. The deferred tax assets and liabilities represent the future tax return consequences of those differences, which will either be deductible or taxable when the assets and liabilities are recovered or settled. Deferred taxes also are recognized for operating losses and tax credits that are available to offset future taxable income.

The standards on accounting for uncertainty in income taxes (incorporated into the FASB Accounting Standards Codification (Codification) Topic 740, Income Taxes, effective for periods ending after September 15, 2009) clarify the accounting and recognition for income tax positions taken or expected to be taken in the Company’s income tax returns. The Company’s income tax filings are subject to audit by various taxing authorities. The Company’s open audit periods are 2008-2011. In evaluating the Company’s tax provisions and accruals, future taxable income, and the reversal of temporary differences, interpretations and tax planning strategies are considered. The Company believes their estimates are appropriate based on facts and circumstances.

Convertible Notes Payable and Warrants – The Company has issued Convertible Promissory Notes (“Notes”). These Notes may be converted at the option of the noteholder into shares of the Company’s common stock. Additionally, these Notes carry warrants for shares of the Company’s common stock. These promissory notes have been recorded as short-term debt (notes payable) in the financial statements, net of any discounts for the conversion and warrant features. The discounts have been amortized on a straight-line basis over the term of each note.

Stock-based compensation - The Company accounts for stock-based compensation in accordance with accounting guidance that requires measuring all stock-based compensation awards at fair value and recognizing an expense in the financial statements. In March 2007, the Company adopted the 2007 Stock Option Plan (“Stock Plan”) for its employees, officers, directors and consultants. The Company has reserved a maximum of 14,000,000 shares of common stock to be issued for stock options or shares of restricted stock under the Stock Plan. We compensate certain employees, officers, directors and consultants with stock-based payment awards and recognize compensation costs for these awards based on their fair values and expense is recognized over the requisite service period. The fair values of certain awards are estimated on the grant date using the Black-Scholes-Merton option-pricing formula, which incorporates certain assumptions including the expected term of an award and expected stock price volatility. Our key assumptions are described in further detail in the Share-Based Payments Note to the Consolidated Financial Statements.

●	Level 1 – Quoted prices in active markets that are unadjusted and accessible at the measurement date for identical, unrestricted assets or liabilities;

●	Level 2 – Quoted prices for identical assets and liabilities in markets that are not active, quoted prices for similar assets and liabilities in active markets, or financial instruments for which significant inputs are observable, either directly or indirectly;

●	Level 3 – Prices or valuations that require inputs that are both significant to the fair value measurement and unobservable.

As of and during the year ended December 31, 2011, we utilized Level 1 inputs to determine the fair value of cash equivalents and we utilized Level 2 inputs to determine the fair value of certain long-lived assets.

Dividends - We have no material operating history and therefore have had no earnings to distribute to stockholders. We currently intend to retain our earnings, if any, and reinvest them in the development and growth of our business and do not foresee payment of a dividend in any upcoming fiscal period.

Net Loss per Common Share - The Company calculates basic loss per share ("EPS") and diluted EPS. Basic loss per share is computed as net loss divided by the weighted average number of common shares outstanding for the period. Diluted EPS would reflect the potential dilution that could occur from common shares issuable through stock options, warrants, and other convertible securities. As of December 31, 2011, 2010 and 2009, the Company had options, warrants and convertible notes to purchase an aggregate of approximately 62 million, 44 million and 32 million shares of common stock, respectively, that were excluded from the calculation of diluted loss per share as their effects would have been anti-dilutive. Therefore, the Company only presents basic loss per share on the face of the statements of operations and in its disclosure of unaudited quarterly financial data in Note 14.

Recent Accounting Pronouncements – In May 2011, the FASB issued updated guidance on fair value measurements. The amendments change the wording used to describe many of the requirements in U.S. GAAP for measuring fair value and for disclosing information about fair value measurements. This guidance is effective during interim and annual periods beginning after December 15, 2011. We will reflect the impact of these amendments beginning with the Company's Quarterly Report on Form 10-Q for the period ending March 31, 2012. The Company does not anticipate a material impact to the Company’s financial position, results of operations or cash flows as a result of this change.

In June 2011, the FASB issued accounting guidance on the Presentation of Comprehensive Income, which requires entities to present reclassification adjustments included in other comprehensive income on the face of the financial statements and allows entities to present the total of comprehensive income, the components of net income and the components of other comprehensive income either in a single continuous statement of comprehensive income or in two separate but consecutive statements. It also eliminates the option for entities to present the components of other comprehensive income as part of the statement of changes in stockholders' equity. This guidance is effective for fiscal years (and interim periods within those years) beginning after December 15, 2011. Adoption of this guidance is not expected to have a material effect on the Company's financial position, results of operations, or cash flows.

In September 2011, the FASB issued updated guidance on the periodic testing of goodwill for impairment, Intangibles—Goodwill and Other. This guidance provides companies with the option to assess qualitative factors to determine if it is more-likely-than-not that goodwill might be impaired and whether it is necessary to perform the two-step goodwill impairment test required under current accounting standards. The authoritative guidance is effective for fiscal years beginning after December 15, 2011. We do not expect the adoption of this guidance to have a material effect on our operating results or financial position.

In December 2010, the FASB issued accounting guidance on Business Combinations regarding how public entities disclose supplemental pro forma information for business combinations that occur during the year. Entities that present comparative financial statements for business combinations must disclose the revenue and earnings of the combined entity as though the business combination that occurred during the current year had occurred as of the beginning of the prior annual reporting period. The authoritative guidance also expanded the disclosures for entities to provide the nature and amount of material, nonrecurring pro forma adjustments directly related to the business combination that is included in the reported pro forma revenue and earnings. The authoritative guidance is effective for business combinations completed in the periods beginning after December 15, 2010 and is applied prospectively as of the date of adoption. We adopted the authoritative guidance on January 1, 2011.

In December 2010, the FASB issued accounting guidance on Intangibles—Goodwill and Other, which requires entities with a zero or negative carrying value to assess, considering qualitative factors, whether it is more likely than not that a goodwill impairment exists, the entity must perform step 2 of the goodwill impairment test. The authoritative guidance does not prescribe a specific method of calculating the carrying value of a reporting unit in the performance of step 1 of the goodwill impairment test. The authoritative guidance is effective for impairment tests performed for fiscal years beginning after December 15, 2010. We adopted the authoritative guidance on January 1, 2011.

In February 2010, the FASB accounting guidance on Amendments to Certain Recognition and Disclosure Requirements, which amends authoritative guidance on certain implementation issues related to the requirement for entities to perform and disclose subsequent events procedures. The authoritative guidance requires SEC filers to evaluate subsequent events through the date the financial statements are available to be issued and exempts SEC filers from disclosing the date through which subsequent events have been evaluated. The authoritative guidance was effective immediately for financial statements that are issued or available to be issued. We adopted the authoritative guidance as of January 1, 2010, and it did not have a material impact on our consolidated financial statements.

In January 2010, the FASB issued an amendment to the fair value measurement and disclosure standard improving disclosures about fair value measurements. The guidance requires additional disclosure for transfer activity pertaining to Level 1 and 2 fair value measurements and purchase, sale, issuance, and settlement activity for Level 3 fair value measurements. The guidance for the Level 1 and 2 disclosures was adopted on January 1, 2010 and did not have an impact on our consolidated financial statements. The guidance for the activity in Level 3 disclosures is effective for fiscal years beginning after December 15, 2010. The Company had no transfers between Level 1, 2 or 3 inputs during the years ended December 31, 2011 and 2010.

Note 3 – Mergers/Acquisitions

On September 15, 2008, the Company consummated the acquisition of Biomass North America Licensing, Inc. (“Biomass”) pursuant to a merger between Biomass and a wholly-owned subsidiary of the Company (with Biomass as the surviving subsidiary of the Company) in accordance with an Agreement and Plan of Merger by and between the Company and Biomass. By virtue of the merger, the Company acquired a license agreement pursuant to which the Company holds a license in the United States and Canada to use patented technology licensed from Biomass North America, LLC, the former parent of Biomass (the “Licensor”), to clean and separate MSW (the “Biomass Recovery Process”). In July 2010, the United States Patent and Trademark Office issued US patent number 7,745,208 for this process (the “BRP Patent”).

Upon consummation of the merger, the Company paid $20,000 in cash and issued a promissory note in the original principal amount of $80,000 bearing interest at an annual rate of 6% (the “Note”) to a shareholder of the Licensor. This note has been paid in full. Additionally, the Company issued to the four shareholders of the Licensor a total of 1,895,000 shares of Common Stock and deposited an additional 4,000,000 shares of Common Stock into an escrow account (collectively, the “Shares”). The Shares were issued as part of the merger consideration received by the shareholders of the Licensor. The escrowed shares will be released to the Licensor’s shareholders if and when the Company commences a commercial development that utilizes the Biomass Recovery Process. The Company recorded a long-term asset of $1.5 million which it will begin to amortize upon utilizing the license in our operations. If the escrowed shares are released based on the specified future events, an increase to the value of the asset will be recorded at that time. Based on the market value of Common Stock as of December 31, 2011, it would result in an increase of approximately $120,000 to the asset. Any future increase in the value of the asset would depend on the market value of our Common Stock at the time of utilization.

Note 4 – Property and Equipment

At December 31, our property and equipment consisted of:

	December 31,
	2011			2010
Computers	$	7,999		$	7,999
Furniture and fixtures		15,799			15,799
Plant and equipment		18,700			18,700
		42,498			42,498
Accumulated Depreciation		(37,715	)		(32,721	)
Total	$	4,783		$	9,777

For the years ended December 31, 2011 and 2010, we had depreciation expense of $4,994 and $10,531, respectively.

Note 5 – Patent

The Company owns US Patent No. 6,306,248 (the “PSC Patent”), which is the underlying technology upon which the BRP Patent is based. The Company acquired the PSC Patent on October 22, 2008 pursuant to a Patent Purchase Agreement (“Agreement”) with World Waste Technologies, Inc. (“WWT”). As part of the acquisition of the PSC Patent, we also became the licensor of such technology under the existing license agreement between Bio-Products International, Inc, the licensee (“Bio-Products”) and WWT. Upon signing the Agreement, the Company paid WWT $150,000, issued a note in the amount of $450,000 (interest at 6.0% per annum and secured by a security interest in the PSC Patent) and issued warrants to purchase 900,000 shares of Common Stock at a price of $0.45 per share and to purchase an additional 900,000 shares of Common Stock at a price of $0.45 per share contingent on payment of the note by July 22, 2009 (the original maturity date). WWT assigned all of its rights, title and interest in the note, warrants, security agreement and purchase agreement to Vertex Energy, Inc. (“Vertex”) as a result of a merger in March 2009. We entered into amendments dated July 23, 2009 whereby: (i) the Company paid 10% of the original note and all accrued interest to date, (ii) all previous warrants (totaling 1,800,000 shares) were reissued at a price of $0.11 per share with no contingencies and (iii) the remaining payments on the note were scheduled to be paid on October 22, 2009 (50% of principal plus accrued interest to date not yet paid) and January 22, 2010 (remaining principal and accrued interest to date). We entered into amendments dated October 22, 2009 whereby: (i) the October 22, 2009 payment was deferred until November 22, 2009 and (ii) we issued additional warrants to Vertex for 500,000 shares of Common Stock at a price of $0.10 per share. The warrants are exercisable at any time for five years from the date of issuance or reissuance. The cost of the PSC Patent acquisition of $600,000 is recorded as a long-term asset on the Balance Sheet. The value of the warrants had been recorded as a contra-balance amount with the note and has been fully amortized, as of March 31, 2010, through interest expense. The note had been recorded as short-term debt (notes payable) in the financial statements, net of the discount for the warrant feature. This note was paid in full in September 2010.

On September 1, 2010, the Company issued a promissory note to CMS Acquisition, LLC (“CMS”) in the amount of $100,000 and bearing interest at 6.0% per annum. The note is secured with a security interest in the PSC Patent. In connection with the financing, the Company issued a warrant to CMS to purchase 2,000,000 shares of the Company’s Common Stock at a price of $0.05 per share. The warrant is exercisable at any time for five years from the date of issuance. The Note was originally to mature on February 28, 2011. The Company and CMS have entered into various amendments extending the due date, the most recent of which was March 27, 2012, which extended the due date to May 15, 2012. As consideration in these amendments, the Company has: (i) paid $25,000 in February 2011 towards accrued interest to date and principal on the Note (ii) increased the interest rate to 10% as of May 15, 2011 and (iii) re-dated the warrants to November 7, 2011.

Note 6 - Technology Licenses

Biomass North America Licensing, Inc.

We own a license in the United States and Canada to use the Biomass Recovery Process (See Note 3 – Mergers/Acquisitions). We recorded a long-term asset of $1.5 million for the value of this license when we acquired the license on September 15, 2008. Amortization of this asset will begin upon commencement of the use of the Biomass Recovery Process. The Company also deposited an additional 4,000,000 shares of the Company’s Common Stock into an escrow account for the benefit of the Licensor. For accounting purposes, the shares remaining in escrow are not considered issued and outstanding as a project has not started using the Biomass Recovery Process. The shares are not deemed issued or vested until that time as described above.

The license requires that the Company pay a royalty in the amount of $1.00 per ton of bone-dry biomass produced using the Biomass Recovery Process. The license agreement is for a term of 21 years or the life of any patent issued for the Biomass Recovery Process. The Company has an exclusive license in the United States and Canada to use the Biomass Recovery Process, except that a principal owner of the Licensor has the right of first offer to manage and operate with respect to any development commenced using the licensed technology within 100 miles of the City of Chicago, Illinois. The license agreement further provides that the Company and the Licensor will work in good faith to complete a commercial development in the City of Chicago using the Biomass Recovery Process.

HFTA, Inc.

On March 20, 2008, the Company entered into a license agreement with HFTA, Inc. (“HFTA”) granting the Company the exclusive worldwide right to use the HFTA technology for the production of ethanol from MSW. The terms in the original agreement required us to pay an initial license fee of $25,000 to HFTA on execution of the agreement and a second license fee of $150,000 on September 1, 2009 if we were using the technology at that time. On August 24, 2009, we entered into an amendment with HFTA that moved the September 1, 2009 payment, plus interest at 6% per annum from the date of the amendment, to March 1, 2010. Additionally, we deposited 2,887,687 shares of our Common Stock into an escrow account on May 12, 2008. The shares held in escrow were released to HFTA as follows: the first third of the shares (962,562 shares) were released from escrow on September 20, 2008 (six months from the date of the original agreement) and the remaining 1,925,125 shares were released upon the amendment in August 2009. As a result, the Company recorded an asset for the value of the first third share payment of approximately $500,000 in September 2008 and recorded an addition to the asset of approximately $190,000 related to the release of the remaining shares in August 2009. During the fourth quarter 2009, the Company decided not to use this technology going forward in our operations and thus have written off the asset as of December 31, 2009. The impairment loss of approximately $690,000 is included in research and development expense on the statement of operations for the year ended December 31, 2009.

Bio-Products International, Inc.

As disclosed in Note 5 - Patent, the Company acquired the PSC Patent in 2008 and as a result, became the licensor to Bio-Products for the PSC Patent pursuant to a Master License Agreement dated as of August 18, 2003 (the “PSC License Agreement”). Pursuant to the terms of the PSC License Agreement, Bio-Products (a wholly-owned subsidiary of Clean Earth Solutions, Inc., “CES”) is the exclusive licensee of the PSC Patent and has the right to sublicense the technology that is part of the PSC Patent (but not the BRP Patent) to any party. In addition, we are entitled to be paid 5% of any revenue derived by Bio-Products from the use of the technology and 40% of any sublicensing fees paid to Bio-Products for the use of the technology. The Master License Agreement is for a term of 20 years that commenced on August 18, 2003. On September 22, 2010, the Company sent a Notice of Breach to Bio-Products. We received a response from Bio-Products on November 5, 2010 disputing our claims. In February 2011, we became aware that Bio-Products effected a transfer of the license in violation of the PSC License Agreement. As a result, on March 21, 2011, we sent a notice of termination to Bio-Products and the transferee terminating the License Agreement. In June 2011, Steve Vande Vegte, a shareholder in CES, filed a lawsuit against various parties, including the Company. The only Cause of Action against the Company is for Declaratory Relief seeking to avoid our March 2011 termination of the license to which Mr. Vande Vegte is not a party. On August 5, 2011, the Company filed a demurrer requesting that the court dismiss the case on the grounds that Mr. Vande Vegte lacks standing to pursue a claim concerning the license and that the claim raised in the complaint is not ripe. The court granted our demurrer to dismiss Cleantech from this lawsuit on December 8, 2011. See Note 12 – Commitments and Contingencies for a further update.

All intangible assets are reviewed for impairment whenever events or other changes in circumstances indicate that the carrying amount may not be recoverable. An impairment charge is recognized if the carrying amount of an intangible asset exceeds its implied fair value.

Note 7 – Debt

	December 31,
	2011			2010

Convertible Notes Payable (2009 Offering), net of discounts of $-0- and $26,595 at December 31, 2011 and December 31, 2010, respectively, which are made up of various individual notes with an aggregate face value of $279,738 and $1,703,329 at December 31, 2011 and December 31, 2010, respectively, due in one year from date of note, interest at 6.0%	$	279,738		$	1,676,734

Convertible Notes Payable (11/10 Offering), net of discounts of $-0- and $-0- at December 31, 2011 and December 31, 2010, respectively, which are made up of various individual notes with an aggregate face value of $1,884,865 and $35,000 at December 31, 2011 and December 31, 2010, respectively, due in one year from date of note, interest at 6.0%		1,884,865			35,000

CMS Acquisition, LLC Note Payable, net of discount of $-0- and $3,492 at December 31, 2011 and December 31, 2010, respectively, with a face value of $77,696 and $100,000 at December 31, 2011 and December 31, 2010, respectively, due on May 15, 2012, interest at 6.0% thru May 15,2011; 10.0% thereafter		77,696			96,508

Convertible Note Payable (6/10 Offering), net of discounts of $-0- and $11,573 at December 31, 2011 and December 31, 2010, respectively, which is made up of one note with a face value of $-0- and $75,000 at December 31, 2011 and December 31, 2010, due in one year from date of note, interest at 12.0%		-			63,427

Total debt		2,242,299			1,871,669
Current maturities		(2,242,299	)		(1,871,669	)
Long-term portion, less current maturities	$	-		$	-

Convertible Notes Payable

Since September 2008, the Company has conducted four offerings of units comprised of a one-year convertible promissory note and a warrant having the terms set forth below:

Offering	Note Interest Rate			Note Conversion Price		Warrant Exercise Price		Closed or Open
2008 Offering		6.0	%	$	0.25	$	0.45	Closed
2009 Offering		6.0	%	$	0.08	$	0.30	Closed
6/10 Offering		12.0	%	$	0.08	$	0.30	Closed
11/10 Offering		6.0	%	$	0.06	$	0.30	Open

Each note may be converted, at the note holder’s option, at any time during the one-year term of the note or prior to the closing of any Qualifying Equity Financing (minimum capital received of $5 million), into shares of Common Stock at the conversion price noted above. All notes have been recorded as short-term debt (notes payable) in the financial statements, net of discounts for the conversion and warrant features (except for the 11/10 Offering which carried no discounts).

11/10 Offering - During November 2010, the Company commenced an offering of units and, as of December 31, 2011, had raised a total of $400,000 of investment proceeds. Two notes were converted during the first quarter of 2011 and one note was converted during the fourth quarter of 2011. As of December 31, 2011, we had $1,884,865 face value of notes outstanding, which includes the exchanged notes from our 2009 Offering. See the Subsequent Events footnote for an update on the continuation of this offering.

CMS Acquisition, LLC Note Payable

In September 2010, the Company issued a note in the amount of $100,000 (interest at 6.0% per annum through May 15, 2011 and 10.0% thereafter, and secured by a security interest in the PSC Patent) and issued warrants to purchase 2,000,000 shares of Common Stock at a price of $0.05 per share. The note is due the earlier of: (i) May 15, 2012 pursuant to an amendment on March 27, 2012 or (ii) the date on which $500,000 or more in the aggregate is raised by the Company in future offerings. The warrants are exercisable at any time for five years from the date of issuance or reissuance (re-dated to November 7, 2011 with an amendment). The value of these warrants has been recorded as a contra-balance amount discount with the note and was amortized (interest expense) through February 28, 2011 (the original due date).

Vertex (formerly WWT) Note Payable

As disclosed previously in Note 5 - Patent, as part of the purchase of the PSC Patent, the Company issued a note in the amount of $450,000 to WWT, which subsequently assigned all of its rights, title and interest in the note, warrants, security agreement and purchase agreement to Vertex Energy, Inc. as a result of a merger in March 2009. This note was paid in full in September 2010. The value of these warrants was recorded as a contra-balance amount discount with the note and was amortized through interest expense over the life of the note.

The discounts on all notes payable have been amortized on a straight-line basis over the term of each note. Amortization of the discounts (included in interest expense in the financial statements) is as follows:

	2011		2010		2009
2008 Offering	$	-	$	7,137	$	523,791
2009 Offering		26,596		253,481		113,344
6/10 Offering		11,573		13,571		-
CMS Acquisition, LLC		3,492		7,222		-
Vertex		-		6,558		178,392
Total amortization	$	41,661	$	287,969	$	815,527

Note 8 - Stockholders' Deficit

During 2009, the Company issued 466,268 shares of Common Stock ($0.25 per share) and 687,500 shares of Common Stock ($0.08 per share) to investors upon their conversions of Convertible Notes.

In August 2009, the Company issued 357,778 shares of Common Stock ($0.13 per share) to the holders of two separate warrants under the Net Issuance clause of the warrant agreements.

In February 2010, the Company issued 150,000 restricted shares of our common stock at $0.10 per share to our newly elected director. The director issued a promissory note to the Company in exchange for the stock purchases similar to the restricted share grants to all other directors. See the share-based footnote for further details.

In April 2010, the Company issued 2,069,375 shares of Common Stock ($0.08 per share) upon the conversion of $140,000 of the Company’s Series A Debentures and accrued interest of approximately $25,000.

In June 2010, the Company issued 133,480 shares of Common Stock ($0.08 per share) to an investor upon the conversion of a Convertible Note.

In August 2010, certain notes receivable from former and current members of our Board of Directors matured. The notes were originally issued in August 2007 to purchase shares of our common stock. Two of the former directors declined to pay these notes or extend the due date. As a result, 300,000 shares of restricted stock, issued at $0.15 per share, were forfeited and cancelled. The two other Directors agreed to extend the due date of their notes to August 2012. As the notes were carried in additional paid-in capital, there was no effect on our financial results for the period from the write-off of these notes.

In January 2011 and February 2011, the Company issued 350,805 and 416,667 shares of Common Stock ($0.06 per share), respectively, to investors upon their conversion of Convertible Notes.

In June and December 2011, separate notes receivable from a consultant matured and were not paid. The notes were originally issued in June 2009 and December 2009 to purchase shares of our common stock. As a result, 625,000 shares of restricted stock, issued at $0.12 per share, and 625,000 shares of restricted stock, issued at $0.06 per share were forfeited and cancelled.

In July 2011, the Company issued 333,333 restricted shares of Common Stock ($0.06 per share) to a consultant in exchange for $20,000 owed in consulting fees to the consultant.

In August 2011, the Company issued 150,000 restricted shares of our Common Stock ($0.055 per share) to each of our non-management Directors (600,000 shares in the aggregate) in recognition of their additional service and assistance to the Company outside of their duties as a member of the Company’s board of directors.

In September 2011, the Company issued 200,000 restricted shares of our Common Stock ($0.05 per share) to a former employee as part of a final settlement agreement.

In December 2011, the Company issued 860,183 shares of Common Stock ($0.06 per share) to an investor upon the conversion of a Convertible Note.

Note 9 - Related Party Transactions

The Company has entered into stock purchase agreements with the executive officers and certain members of the Board of Directors. The executive officers and directors issued notes to the Company in exchange for their stock purchases. These notes and accumulated interest are recorded as notes receivable in Stockholders’ Deficit.

The Company had engaged the law firm of Sauerwein, Simon and Blanchard (“SSB”) related to various issues including our reverse merger, our SB-2 registration statement, litigation matters and general business activity. A member of our board of directors is a partner of SSB. We no longer use SSB as legal counsel and have incurred less than $100 in legal fees since January 2010. As of December 31, 2011, all amounts have been paid to SSB except for approximately $90,000.

The Company uses the Crane Agency (“Crane”) as its broker for business and property insurance. Our CEO’s brother was employed by Crane and involved in the negotiation of coverage and premiums related to policies purchased through December 31, 2010 (when his employment with Crane ended). The Company paid less than $3,000 for the years ended December 31, 2011 and 2010 in commissions on policies placed by Crane.

Beginning in 2009, the Company has provided advances to two employees – Ed Hennessey and Mike Kime. Mr. Kime resigned from his positions with the Company effective June 21, 2010. As of December 31, 2011 and 2010, the aggregate balances of advances totaled approximately $30,000 and $20,000, respectively. The balances are included in Prepaids and Other Current Assets on the Balance Sheet.

Three members of our Board of Directors, Dr. Jackson Nickerson, Mr. Jose Bared, Sr. and David Bransby are parties in investments made in our convertible note offerings. As of December 31, 2011 and December 31, 2010, the aggregate amount due on these investments, including interest, is approximately $650,000 and $613,000, respectively. Mr. Bared, Mr. Bransby and Dr. Nickerson have agreed to exchange all of their notes into our 11/10 Offering, except one for $50,000 for Dr. Nickerson. He has put the company on notice of his demand for payment and intent not to exchange this note. As of December 31, 2011, this note has not been repaid.

Note 10 – Share-based Payments

The Company recognizes share-based compensation expense for all share-based payment awards including stock options and restricted stock issued to employees, directors and consultants and is measured at the grant date, based on the estimated fair value of the award, and is recognized as expense over the requisite service period. The Company has no awards with market or performance conditions.

In March 2007, the Company adopted the 2007 Stock Option Plan (“Stock Plan”) for its employees, directors and consultants, which includes an equity compensation plan for non-employee directors pursuant to which stock options and shares of restricted stock may be granted. The Company currently has reserved a maximum of 14,000,000 shares of common stock to be issued for stock options or restricted shares awarded under the Stock Plan.

The estimated fair value of stock option grants is computed using the binomial option-pricing model. Generally, expected volatility is based on historical periods commensurate with contractual term of options. However, since we have no history of stock price volatility as a public company at the time of the grants, we calculated volatility by considering historical volatilities of public companies in our industry. Due to the short history of our industry, the historical period used in our calculations is shorter than the contractual term of the options. The fair value for options granted was determined at the date of grant. The following assumptions were used for options granted in the corresponding year.

	For the years ended December 31,
	2011			2010			2009
Risk-free interest rate		.98%-2.28	%		1.76%-2.58	%		2.44	%
Dividend yield		0	%		0	%		0	%
Volatility		19.75%-21.8	%		24.3%-28.9	%		29.58	%
Expected term (years)		5.0			5.0			5.0
Weighted-average Fair Value	$	0.01		$	.02-$.03		$	0.03

Stock option expense is recognized in the statements of operations ratably over the vesting period based on the number of options that are expected to ultimately vest. Our options have characteristics significantly different from those of traded options and changes in the assumptions can materially affect the fair value estimates. The following table presents the components of share-based compensation recorded as general and administrative expense.

	For the Year Ended December 31,
	2011		2010		2009
Pre-tax compensation expense:
Stock options	$	39,989	$	118,361	$	361,721
Warrants		-		-		-
Total expense		39,989		118,361		361,721
Tax benefit, net		-		-		-
After-tax compensation expense	$	39,989	$	118,361	$	361,721

Related to all grants, the Company will record future compensation expense for stock options of approximately $15,000 for 2012. The potential tax benefit realizable for the anticipated tax deductions of the exercise of share-based payments pertaining to stock options totaled approximately $300,000 at December 31, 2011. However, due to the uncertainty that the tax benefits will be realized, these potential benefits were not recognized currently.

As of December 31, 2011, there was approximately $25,000 of unrecognized compensation cost related to all share-based payment arrangements, which will be recognized over a remaining period of approximately 2.3 years. There are 3,705,000 options granted that are not yet vested as of December 31, 2011. These options have a weighted average exercise price of $0.05.

A summary of the Company's stock option activity and related information as of and for the three years ended December 31, 2011, is set forth in the following table:

	Shares Under Option			Weighted Average Exercise Price		Aggregate intrinsic value
Options outstanding at December 31, 2008		6,510,000		$	0.19		(1)
Granted		305,000			0.10
Options outstanding at December 31, 2009		6,815,000			0.19		(1)
Granted		322,000			0.07
Forfeited		(1,600,000	)		0.26
Options outstanding at December 31, 2010		5,537,000			0.16		(1)
Granted		4,310,000			0.05
Forfeited		(25,000	)		0.10
Options outstanding at December 31, 2011		9,822,000			0.11		(1)

Options exercisable at December 31, 2011		6,117,000		$	0.13		(1)

(1) The weighted-average exercise price at December 31, 2011, 2010 and 2009 for all options was greater than the fair value of the Company's common stock on that date, resulting in an aggregate intrinsic value of $-0-.

The following table summarizes information about the Company's issuances of restricted stock for the three years ended December 31, 2011:

	Restricted Shares Issued			Weighted-Avg Exercise Price
Balance as of December 31, 2008		780,000		$	0.20
Granted		1,550,000			0.09
Balance as of December 31, 2009		2,330,000			0.13
Granted		150,000			0.10
Forfeited		(300,000	)		0.15
Balance as of December 31, 2010		2,180,000			0.12
Granted		600,000			0.06
Forfeited		(1,310,000	)		0.10
Balance as of December 31, 2011		1,470,000			0.10

Restricted stock vested at December 31, 2011		1,465,833		$	0.11

Note 11 – Income Taxes

The Company recognizes deferred income tax liabilities and assets for the expected future tax consequences of events that have been recognized in the financial statements or tax returns. Under this method, deferred tax liabilities and assets are determined based on the differences between the financial statement carrying amounts and the tax basis of assets and liabilities using enacted tax rates in effect in the years in which the differences are expected to reverse.

The Company incurred no income taxes for the years ended December 31, 2011, 2010 and 2009. The expected income tax benefit and resulting deferred tax asset for the years ended December 31, 2011, 2010 and 2009 is approximately $280,000, $460,000 and $1,086,000, respectively. These benefits are the result of temporary differences (start-up costs, stock compensation and other items) and operating loss carryforwards. The difference between the expected income tax benefit and non-recognition of an income tax benefit in each period is the result of a valuation allowance applied to deferred tax assets. A valuation allowance in the same amount of the benefit has been provided to reduce the deferred tax asset, as realization of the asset is not assured.

At December 31, 2011, net operating loss carryforwards of approximately $18,000, $182,000 $630,000, $928,000, and $74,000 are available to offset future taxable income and expire in 2026, 2027, 2028, 2029 and 2030, respectively. This results in a net deferred tax asset of approximately $730,000 for which the Company has recorded a full valuation allowance. The net operating loss carryforwards may be limited under the Change of Control provisions of the Internal Revenue Code section 382.

Temporary differences which give rise to net deferred tax assets at December 31, 2011 and 2010 are:

	At December 31,
	2011			2010
Start-up costs	$	642,000		$	580,000
Net operating loss carryforward		730,000			730,000
Accrual to cash conversion		1,008,000			801,000
Share-based compensation related to stock options		303,000			287,000
Other		4,000			8,000
Total		2,687,000			2,406,000
Valuation allowance		(2,687,000	)		(2,406,000	)
Net deferred tax asset	$	-		$	-

Note 12 – Commitments and Contingencies

Contingencies

As disclosed previously in Note 6 – Technology Licenses, in June 2011, Steve Vande Vegte, a shareholder in CES, filed a lawsuit against various parties, including the Company. The only Cause of Action against the Company is for Declaratory Relief seeking to avoid our March 2011 termination of the license to which Mr. Vande Vegte is not a party. On August 5, 2011, the Company filed a demurrer requesting that the court dismiss the case on the grounds that Mr. Vande Vegte lacks standing to pursue a claim concerning the license and that the claim raised in the complaint is not ripe. On December 8, 2011, the demurrer to dismiss Cleantech was granted. In October 2011, a Cross-Complaint was filed by Clean Conversion Technologies, Inc. (“CCT”) and Michael Failla v. Cleantech Biofuels, Inc. CCT is asking that the Company’s termination of the license agreement is void. On January 30, 2012, CCT filed an anti-trust lawsuit against the Company and Mr. Vande Vegte alleging monopolistic and anti-competitive acts to conspire to completely eliminate competition in an emerging line of commerce known as PSC conversion, which is a patented process owned by Cleantech (the PSC technology). On March 26, 2012, the Company filed a motion to dismiss. The hearing is currently set for May 7, 2012. We intend to vigorously defend our rights. In view of the inherent difficulty of predicting the outcome of litigation and claims, the Company often cannot predict what the eventual outcome of the pending matters will be, what the timing of the ultimate resolution of these matters will be, or what the eventual loss, fines or penalties related to each pending matter may be. We believe that these matters will not have a material adverse effect on the Company’s financial position, results of operations or cash flows. However, an adverse outcome could be material to the Company’s results of operations or cash flows for any particular reporting period.

Commitments

Lease – The Company’s lease to rent approximately 1,800 square feet of office space for use as our corporate office, located at 7386 Pershing Ave. in St. Louis, Missouri has expired. We are currently in the process of extending this lease while occupying the space. Our monthly rent under the lease is $1,800 plus the cost of utilities.

Note 13 – Subsequent Events

Convertible Notes Payable

In connection with our 11/10 Offering, which is still open, we have raised a total of $435,000 of investment proceeds as of March 23, 2012.

All of the promissory notes in our 2009 Offering are now due. Certain notes have been refinanced to our 11/10 Offering, converted to shares of our common stock or repaid. Additionally, some notes in our 11/10 Offering are also now due. As of March 23, 2012, approximately $420,000 is currently due in the aggregate, including interest. We are working with each remaining noteholder to exchange, convert or repay these promissory notes.

CMS Acquisition, LLC Note Payable

Pursuant to an amendment on March 27, 2012, the due date of the note has been extended to the earlier of: (i) May 15, 2012 (extended from February 7, 2012) or (ii) the date on which $500,000 or more in the aggregate is raised by the Company in future offerings.

Note 14 – Quarterly Financial Data (Unaudited)

The results of operations by quarter were as follows:

	For the quarters ended 2011:
	Mar 31			June 30		Sept 30			Dec 31
Costs and expenses:
General and administrative	$	117,843		$	97,481	$	142,755		$	108,631
Professional fees		43,264			18,040		31,395			33,167
		161,107			115,521		174,150			141,798
Other expense (income):
Interest		58,993			47,196		34,951			35,425
Other (income) expense		(3,832	)		3,958		(2,953	)		(45,601	)

Net loss applicable to common stockholders	$	216,268		$	166,675	$	206,148		$	131,622

Basic net loss per common share		**			**		**			**

** - less than $.01 per share

	For the quarters ended 2010:
	Mar 31			June 30			Sept 30		Dec 31
Costs and expenses:
General and administrative	$	195,401		$	241,350		$	155,019	$	99,658
Professional fees		41,524			32,946			32,988		(16,231	)
		236,925			274,296			188,007		83,427
Other expense (income):
Interest		119,518			104,626			101,302		81,751
Other (income) expense		(4,291	)		(4,439	)		4,377		(3,866	)

Net loss applicable to common stockholders	$	352,152		$	374,483		$	293,686	$	161,312

Basic net loss per common share	$	0.01		$	0.01			**		**

** - less than $.01 per share

ITEM 9. CHANGES IN AND DISAGREEMENTS WITH ACCOUNTANTS ON ACCOUNTING AND FINANCIAL DISCLOSURE

None.

ITEM 9A. CONTROLS AND PROCEDURES

EVALUATION OF DISCLOSURE CONTROLS AND PROCEDURES

Effectiveness of Disclosure Controls and Procedures – We maintain a set of disclosure controls and procedures designed to ensure that information required to be disclosed in our reports filed under the Securities Exchange Act of 1934, as amended, is recorded, processed, summarized and reported within the time periods specified by the Security and Exchange Commission’s rules and regulations. Disclosure controls are also designed with the objective of ensuring that this information is accumulated and communicated to our management, including our chief executive officer and chief financial officer, as appropriate, to allow timely decisions regarding required disclosure.

Our management does not expect that our disclosure controls and procedures will necessarily prevent all fraud and material error. Our disclosure controls and procedures are designed to provide reasonable assurance of achieving the objectives outlined above. Based on their most recent evaluation, our chief executive officer and chief financial officer concluded that our disclosure controls and procedures are effective at that reasonable assurance level at December 31, 2011. Further, the design of a control system must reflect the fact that there are resource constraints, including, but not limited to having two total employees (chief executive officer and chief financial officer), and the benefits of controls must be considered relative to their costs. Because of the inherent limitations in all control systems, no evaluation of controls can provide absolute assurance that all control issues and instances of fraud, if any, within the Company have been detected. These inherent limitations include the realities that judgments in decision-making can be faulty, and that breakdowns can occur because of simple error or mistake.

Management’s Report on Internal Control Over Financial Reporting – Our management is responsible for establishing and maintaining adequate internal control over financial reporting as such term is defined in Rules 13a-15(f) and 15d-15(f) of the Securities Exchange Act of 1934. Internal control over financial reporting provides reasonable assurance of the reliability of our financial statements for external purposes in accordance with generally accepted accounting principles in the United States of America. Internal control involves maintaining records that accurately represent our business transactions, providing reasonable assurance that receipts and expenditures of company assets are made in accordance with management authorization, and providing reasonable assurance that unauthorized acquisition, use or disposition of company assets that could have a material effect on our financial statements would be detected or prevented on a timely basis.

Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatement. Also, projections of any evaluation of effectiveness to future periods are subject to risk that controls may become inadequate because of changes in condition, or that the degree of compliance with the policies or procedures may deteriorate.

Management conducted an evaluation of the effectiveness of our internal control over financial reporting based on the framework in Internal Control — Integrated Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission (COSO). Based on this evaluation under the framework in Internal Control — Integrated Framework, our management concluded that our internal control over financial reporting was effective as of December 31, 2011 . The effectiveness of the Company’s internal control over financial reporting as of December 31, 2011, has not been audited by Milhouse & Neal, LLP, an independent registered public accounting firm, as there was no Securities and Exchange Commission requirement for Cleantech Biofuels, Inc. to obtain this audit as of December 31, 2011.

Changes in Internal Control Over Financial Reporting – During the three months ended December 31, 2011, there were no material changes in the Company’s internal control over financial reporting that have materially affected, or are reasonably likely to materially affect, the Company’s internal control over financial reporting.

Attestation Report of Registered Public Accounting Firm - This annual report does not include an attestation report of our registered public accounting firm as such report is not required due to established rules of the Securities and Exchange Commission for smaller reporting companies.

ITEM 9B. OTHER INFORMATION

None.

PART III

ITEM 10. DIRECTORS, EXECUTIVE OFFICERS AND CORPORATE GOVERNANCE

The Company’s Restated Articles of Incorporation, as amended, and Amended and Restated By-laws provide for a division of the Board of Directors into three classes. One of the classes is elected each year to serve a three-year term. The Company’s Amended and Restated By-Laws currently specify that the number of directors shall be not less than three nor more than nine, subject to amendment by the Board of Directors. Currently, the Company has five members of the Board of Directors as detailed below.

The following table sets forth for each director and officer, such director’s or officer’s age, principal occupation for at least the last five years, present position with the Company, the year in which such director or officer was first elected or appointed (each director serving continuously since first elected or appointed), directorships with other companies whose securities are registered with the SEC, and the class of such director.

Class III Director: Terms expiring in 2013

Name		Age		Principal Occupation		Service as Director Since
Edward P. Hennessey		53		Mr. Hennessey currently is Chief Executive Officer and President of the Company, and serves as Chairman of the Board of Directors. Mr. Hennessey has been the President and CEO of SRS Energy since 2003 and served as President of Supercritical Recovery Systems, Inc. prior to that time since 2002. Mr. Hennessey began his career in Finance with Shearson Lehman Brothers in 1986 and worked in the securities industry from 1986 until 2000.		2007

Class I Directors: Terms expiring in 201 4

Name	Age	Principal Occupation	Service as Director Since
Paul Simon, Jr.	53	Mr. Simon is a licensed attorney practicing in St. Louis, Missouri and has been a partner in the firm, Sauerwein, Simon, & Blanchard, P.C. since 2006. Prior to that time, he was a partner with the firm Helfrey, Simon and Jones, P.C. from 1991 until 2006. Mr. Simon is a graduate of the University of Missouri where he received his B.S. in Business Administration and St. Louis University School of Law where he received his J.D.	2007
Jose Bared, Sr.	70	Mr. Bared began his career as an engineer and in 1968 founded The Bared Company, a Mechanical and Electrical Engineering and Design company. Mr. Bared was also a member of the founding group that purchased Republic National Bank of Miami in 1971. Mr. Bared served as a director of the bank from 1971 until its sale in 1998. Currently Mr. Bared serves on the Board of Directors of Jackson – United Petroleum, a natural gas producer operating in Kentucky and Pennsylvania. He has served on the Board of Trustees for the University of Miami for the past 30 years. He also has served on the Board of Governors of the Sylvester Cancer Center for the past 15 years and is a life member of the center. Mr. Bared holds a B.S. in Mechanical Engineering from the University of Miami.	2010

Class II Directors: T erms expiring in 2012

Name	Age	Principal Occupation	Service as Director Since
Jackson Nickerson, Phd	49	Dr. Nickerson is the Frahm Family Professor of Organization and Strategy at Washington University's Olin Business School in St. Louis and has been at the university since 1996. He consults with numerous profit and not-for-profit organizations on strategy development. Dr. Nickerson launched and is currently a director of nformd.net, a privately held new media company. He has a B.S. in mechanical engineering from Worcester Polytechnic Institute and an M.S. in mechanical engineering, an M.B.A. and a Ph.D. from the University of California, Berkeley.	2009

David Bransby, Phd	60	Dr. Bransby is a Professor of Energy Crops and Bioenergy in the Department of Agronomy and Soils at Auburn University where he has taught and conducted research since 1987. He has more than 30 years of experience in agronomic research, and has spent over 20 years specializing in the production and processing of energy crops. He serves on the editorial boards of two international bioenergy journals, and consults for several private bioenergy companies	2009

Name	Age	Principal Occupation	Service as Officer Since
Thomas Jennewein	48	Mr. Jennewein is currently the Chief Financial Officer of the Company. Previously he served as Manager of Financial Reporting for the Maverick Tube Corporation from 2005-2007 and as Manager of Financial Reporting for the Argosy Gaming Company from 2000-2005.	2007

Audit Committee

The Audit Committee is currently comprised of Messrs. Nickerson (Chairman) and Bransby, each of whom is “independent” in accordance with the Nasdaq standards, as well as the independence requirements for audit committee members under Rule 10A-3 promulgated under the Exchange Act. In addition, the Company has determined that Mr. Nickerson is qualified as an “audit committee financial expert” as that term is defined in the rules of the SEC. The Audit Committee evaluates significant matters relating to the audit and internal controls of the Company, reviews the scope and results of the audits conducted by the Company’s independent public accountants and performs other functions or duties provided in the Audit Committee Charter. During the 2011 fiscal year, the Audit Committee held one meeting.

Compensation Committee

Our Compensation Committee and Compensation Committee Charter have been eliminated and replaced by the Board of Directors, whom now perform duties including reviewing the Company’s remuneration policies and practices, executive compensation and administering the Company’s stock option plan.

Nomination of Directors

The Board of Directors does not currently have a standing Nominating Committee or a charter regarding the nominating process. The Board of Directors will give appropriate consideration to written recommendations from stockholders regarding the nomination of qualified persons to serve as directors of the Company, provided that such recommendations contain sufficient information regarding proposed nominees so as to permit the independent members of the Board of Directors to properly evaluate each nominee’s qualifications to serve as a director. Nominations must be addressed to the Secretary of the Company at 7386 Pershing Ave, University City, MO 63130. The Board of Directors may also conduct their own search for potential candidates that may include candidates identified directly by a variety of means as deemed appropriate by the independent directors.

There are no established term limits for service as a director of the Company. In general, it is expected that each director of the Company will have the highest personal and professional ethics, integrity and values and will consistently exercise sound and objective business judgment. In addition, it is expected that the Board of Directors as a whole will be made up of individuals with significant senior management and leadership experience, a long-term and strategic perspective and the ability to advance constructive debate.

Code of Ethics

All directors, officers and employees of the Company, including its Chief Executive Officer and its Chief Financial Officer, are required to comply with the Company’s Code of Ethics to ensure that the Company’s business is conducted in a legal and ethical manner. The Code of Ethics covers all areas of business conduct, including employment policies and practices, conflict of interest and the protection of confidential information, as well as strict adherence to all laws and regulations applicable to the conduct of our business. Directors, officers and employees are required to report any conduct that they believe in good faith to be an actual or apparent violation of our Code of Ethics. The Company, through the Audit Committee, has procedures in place to receive, retain and treat complaints received regarding accounting, internal accounting control or auditing matters and to allow for the confidential and anonymous submission of concerns regarding questionable accounting or auditing matters. The Company’s Code of Ethics was filed as Exhibit 14 in its December 31, 2007 Form 10-KSB filed with the Securities and Exchange Commission on March 28, 2008 and can be obtained free of charge by written request to the attention of the Secretary of the Company at 7386 Pershing Ave, University City, MO 63130 or by telephone at (314) 802-8670. Any changes to or amendments of the Code of Ethics will be filed as a future Exhibit in our filings.

ITEM 11. EXECUTIVE COMPENSATION

Compensation Discussion and Analysis

Two key aspects of the duties and responsibilities of the Board of Directors are the administration of our compensation programs, including our equity incentive program, and the approval of compensation for our executive officers. The Board of Directors has the authority to retain outside counsel and/or such other experts or consultants as it deems necessary to discharge its duties.

Our Executive Compensation Policy

We believe that a critical factor in attracting and retaining talented and dedicated management that is necessary for our success is the establishment and fair implementation of a comprehensive executive compensation program. Accordingly, our overall compensation philosophy is to offer our executives and other members of our management team compensation and benefits that meet and enhance our goals of attracting, retaining and motivating highly skilled people to work together as a team to achieve our financial and strategic business objectives. In furtherance of this compensation philosophy, our executive compensation program is designed to:

●	provide fair and reasonable compensation that meets the competitive environment for executive talent;
●	help motivate the members of our executive team for excellent performance; and
●	align the interests of our executive team members with those of our stockholders and the long-term success of our company.

While all decisions regarding executive compensation are ultimately made by our Board of Directors, they also rely on the recommendations of the Chief Executive Officer with respect to all of our executive officers (other than the Chief Executive Officer himself), particularly with regard to his assessment of each executive officer’s individual performance against achievement of strategic objectives, level of responsibility exercised and the level of specialized experience and knowledge required to do the job. Determinations by our Board of Directors are not made in accordance with strict formulas which measure weighted qualitative and quantitative factors. Rather, such determinations are more subjective in nature and take into account not only the recommendations of our Chief Executive Officer, but such other factors as deemed relevant in an effort to blend competitive ranges into our own internal policies and practices. The Board of Directors may also seek advice from a compensation consultant.

All of our executive officers have entered into three-year employment agreements with the Company effective as of August 31, 2007 that provide for, among other things, the base salary, if any, of such executive officer’s compensation package. These employment contracts permit us to increase, but not decrease, base salaries within the contract term. The contracts expired on August 31, 2010 and by their terms, automatically renew for additional one-year periods, unless terminated by either the Company or the employee.

Elements of our Executive Compensation Program

Our executive officer program consists of three basic elements: base salary, annual incentive bonus, and long-term incentive compensation. Currently our executive officers whose compensation is reported in the Summary Compensation Table are paid their approved salaries as cash is available and have not been paid any bonus. We expect that in the future we will begin paying the Named Executive Officers salary and bonuses consistent with their position and job performance. Consistent with our executive officer compensation philosophy, we have structured each element of our compensation package as follows:

Base Salary - In December 2008, annual base salaries, effective beginning November 2008, were approved of $144,000 for Mr. Hennessey and $120,000 for Mr. Jennewein. In addition, Mr. Hennessey was paid $56,000 during 2008 under a previous employment agreement. Salaries are currently paid based on cash availability. Currently, the salaries paid to our executive officers as a group are substantially less than the salaries typically paid to executives with the experience and background of our executive officers.

Bonuses - None of our executive officers were paid a bonus in 2011, 2010, or 2009. We do not currently have any bonus plan for executive officers.

Long-Term Incentive Compensation - The long-term incentive awards for our executive officers are made under our 2007 Stock Option Plan under which the Board of Directors may, among other things, grant or award stock options and other stock-based awards, subject to certain limitations and restrictions as set forth in the plan. Our use of stock-based awards for our executive officers is the primary means by which we provide our executive officers a long-term incentive that becomes more valuable to the executive to the extent our share value increases, thereby aligning each executive’s interest with the interest of our stockholders.

It is the policy of the Board of Directors that, with respect to all equity-based compensation for the executive officers, the award dates for each grant shall be specified by the Board of Directors at a duly convened meeting as of a date on or after the date of its action, and that the exercise price or value of the grant shall be determined by reference to the closing price of our common stock on the specified award date. See “Outstanding Equity Awards at Fiscal Year-End” table for additional information. Equity grants may also be made to new executive officers upon commencement of their employment and, on occasion, to executive officers in connection with a significant change in job responsibility, extraordinary performance, or other reasons.

Executive Perquisites - Historically, we have not offered perquisites to our executive officers.

Tax and Accounting Implications

Section 162(m) of the Internal Revenue Code generally precludes a public company from taking a federal income tax deduction for annual compensation in excess of $1 million per individual paid to its chief executive officer or the other named executive officers. Under Section 162(m), certain compensation, including “performance-based compensation,” is excluded from this deduction limitation. Our intent is to structure compensation paid to our executives to be deductible; however, from time to time, the Board of Directors may award compensation that may not be deductible if it determines that such awards are consistent with our compensation philosophy and in the best interest of our stockholders. We believe that all of the 2011 compensation paid to our executive officers is fully deductible.

Summary Compensation Table

The following table summarizes the total compensation paid or earned by the Company’s Principal Executive Officer and Principal Financial Officer, the only executive officers of the Company (together the “Named Executive Officers”), who served these positions during 2011.

				(1) Stock
Name and Principal Position(s)	Year	Salary ($)		Options ($)		Total ($)
Edward P. Hennessey, President and CEO	2008	$	68,000	$	103,574	$	171,574
	2009		109,000		227,182		336,182
	2010		15,500		75,271		90,771
	2011		17,500		25,154		42,654
Thomas Jennewein, Chief Financial Officer	2008		10,000		36,623		46,623
	2009		92,000		45,880		137,880
	2010		13,500		18,444		31,944
	2011		20,500		11,680		32,180

(1)	The assumptions made when calculating the amounts in this column are found in footnote 10 to the Consolidated Financial Statements included in this report. The amounts represent the accounting cost in accordance with U.S. GAAP that the Company recorded in its Statements of Operations in each year.

Outstanding Equity Awards at Fiscal Year-End

The following table provides information on stock options and restricted stock awards granted to the Named Executive Officers that were outstanding as of December 31, 2011. The market values in this table were computed using the closing price of the Company’s common stock on December 31, 2011, which was $0.03.

	Option Awards									Stock Awards
	Grant Date	Number of Securities Underlying Unexercised Options (#) - Exercisable			Number of Securities Underlying Unexercised Options (#) - Unexercisable (3)		Option Exercise Price ($)		Option Expiration Date	Number of Shares or Units of Stock that have vested (#)			Market value of shares or units of stock that have vested
Edward P. Hennessey	8/31/2007		2,250,000	(1)		-	$	0.15	8/31/2014				$	-
	12/4/2008		1,200,000	(2)		-	$	0.15	12/4/2015				$	-
	12/4/2008										60,000	(4)	$	-
	8/25/2011		-	(6)		2,200,000	$	0.055	8/25/2018				$	-
Thomas G. Jennewein	8/31/2007		800,000	(1)		-	$	0.15	8/31/2014				$	-
	12/4/2008		400,000	(2)		-	$	0.36	12/4/2015				$	-
	12/4/2008										60,000	(4)	$	-
	7/6/2010		162,000	(5)		-	$	0.07	7/6/2017				$	-
	1/4/2011		500,000	(7)		250,000	$	0.05	1/4/2018				$	-
	8/25/2011		-	(6)		750,000	$	0.055	8/25/2018				$	-

(1)

(2)

(3)

(4)

(5)

(6)

(7)

This option grant vested in three equal annual installments beginning on August 31, 2008.

This option grant vested in three equal annual installments beginning on August 31, 2009.

The options shown in this column are nonvested as of December 31, 2011.

This stock award was granted on December 4, 2008. Each officer issued promissory notes with an exercise price of $0.36.

This stock award was granted on July 6, 2010 and vested immediately.

This option grant vests in three equal annual installments beginning on August 31, 2012.

This option grant vests in three equal installments on January 4, 2011; August 31, 2011 and August 31, 2012.

Option Exercises and Stock Vested

	Option Awards									Stock Awards
	Number of Shares Acquired on Exercise (#)		Value Realized on Exercise ($)		Number of Shares Acquired on Vesting (#)		Value Upon Vesting ($) (1)			Number of Shares Acquired on Vesting (#)		Value Realized on Vesting ($)
Edward P. Hennessey		-	$	-		750,000	$	562,500			60,000	$	-
		-	$	-		1,500,000	$	-	(2)
		-	$	-		1,200,000	$	-	(2)
Thomas G. Jennewein		-	$	-		266,667	$	200,000			60,000	$	-
		-	$	-		533,333	$	-	(2)
		-	$	-		400,000	$	-	(2)
		-	$	-		162,000	$	-	(2)
		-	$	-		500,000	$	-	(2)

(1)	The values reflect the market value of Cleantech Biofuels, Inc. common stock as of the vesting dates. These prices ranged from $0.03 to $0.90.

(2)	The price of our common stock on these vesting dates was less than or equal to the exercise price of the options.

Pension Benefits - None of our Named Executive Officers are covered by a defined benefit pension plan or other similar benefit plan that provides for payments or other benefits.

Nonqualified Deferred Compensation - We do not have any nonqualified deferred compensation plans.

Director Compensation – Each of the Company’s non-employee directors received compensation of 150,000 restricted shares of the Company’s common stock and a grant of 90,000 options (two-year vesting period) in 2011. Each non-employee board member receives a grant of 40,000 options and 150,000 restricted shares of company common stock upon beginning as a director of the Company. The Company’s non-employee directors received no salary or other compensation as a board or committee member in 2011, 2010 and 2009.

Potential Payments Upon Termination or Change-in-Control

Each of the employment agreements with our Named Executive Officers was entered into for an initial term of employment that commenced as of August 31, 2007 and expired on August 31, 2010. By their terms, the employment agreements automatically renew for additional one-year periods, unless terminated by either the Company or the employee.

The employment agreements may be terminated upon: (i) the Company’s dissolution, (ii) the death or permanent disability of the employee, (iii) by the Company upon the employee’s unsatisfactory performance of his duties under the agreement, (iv) ten days’ written notice by the Company upon breach or default of the terms of the agreement by the employee, or (v) by the employee upon 30 days’ written notice to us. The employment agreements also permit the Company to terminate the employee’s employment following an act of misconduct.

If employment is terminated for any of the reasons set forth above, the Named Executive Officers discussed above will only receive their base salary accrued but unpaid as of the date of the termination. If employment is terminated for any reason other than those set forth above and those subsequent to a change in control of the Company, as discussed below, the Officers will receive one year of base salary. Additionally, all of Mr. Hennessey’s and Mr. Jennewein’s shares subject to stock options will vest.

If, pursuant to a change in control of the Company, an employee’s employment agreement is involuntarily terminated, the employee will receive severance pay in an amount equal to his annual base salary for one year following the date on which he was terminated.

ITEM 12. SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT AND RELATED STOCKHOLDER MATTERS

The following table sets forth information as of December 31, 2011 with respect to each person or group known by the Company to be the beneficial owner of more than five percent of its outstanding shares of Common Stock. Beneficial ownership of shares has been determined in accordance with Rule 13d-3 of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), under which a person is deemed to be the beneficial owner of securities if he or she has or shares voting or investment power with respect to such securities or has the right to acquire ownership thereof within 60 days. Accordingly, the amounts shown in the tables do not purport to represent beneficial ownership for any purpose other than compliance with the reporting requirements of the SEC.

Name and Address of Beneficial Owner	Amount and Nature of Beneficial Ownership		Percent of Class
Edward P. Hennessey, Jr. (1) 7310 Forsyth Ave., Unit 104 Clayton, MO 63105		7,443,275		10.7	%
SRS Legacy Trust (2) 147 N. Meramec, Suite 200 Clayton, MO 63105		6,972,214		10.0	%
RAM Resources, L.L.C. (3) 13397 Lakefront Drive Earth City, Missouri 63045		4,236,089		6.1	%

(1)	Amount represents shares owned by Supercritical Recovery Systems, Inc., of which Mr. Hennessey serves as President and a Member of the Board of Directors.

(2)	SRS Legacy Trust is an irrevocable trust of which Edward P. Hennessey, Jr. is a beneficiary. Michael Hennessey, Mr. Hennessey’s brother, has sole voting power, and Paul Simon, Jr., one of our directors, has sole dispositive power with respect to these shares.

(3)	Rodney H. Thomas, as Trustee of the Trust which is the majority owner of RAM Resources, L.L.C., has controlling voting and dispositive power over these shares.

SECURITY OWNERSHIP OF MANAGEMENT

Under regulations of the SEC, persons who have power to vote or to dispose of our shares, either alone or jointly with others, are deemed to be beneficial owners of those shares. The following table sets forth, as of December 31, 2011, the beneficial ownership of the outstanding Common Stock of each current director, each of the executive officers named in the Summary Compensation Table set forth herein and the executive officers and directors as a group. Unless otherwise noted, the Company believes that all persons named in the table below have sole voting power and dispositive power with respect to all shares beneficially owned by them.

Name and Address of Beneficial Owner	Amount and Nature of Beneficial Ownership			Percent of Class
Edward P. Hennessey, Jr.		10,953,275	(1)		15.0	%
Thomas Jennewein		1,922,000	(2)		2.7	%
Jackson Nickerson		391,151	(3)		*	%
David Bransby		340,000	(2)		*	%
Jose Bared		340,000	(2)		*	%
Paul Simon		417,935	(3)		*	%
Total owned by All Executive Officers and Directors		14,364,361			19.1	%

*Less than 1%.

(1)	Includes the shares described in footnote 1 to the “Security Ownership of Certain Beneficial Owners” table and the vested portion and the portion that will vest within 60 days hereof of shares of options and restricted stock.

(2)	Amounts represent the vested portion and the portion that will vest within 60 days hereof of shares of options and restricted stock.

(3)	Amount includes the vested portion and the portion that will vest within 60 days hereof of shares of options and restricted stock and shares held individually.

We currently have 14,000,000 shares of our common stock approved under our 2007 Stock Option Plan. See Part II, Item 5 for the table reflecting shares issued and available.

ITEM 13. CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS AND DIRECTOR INDEPENDENCE

From time to time, the Company has engaged in various transactions with certain of its directors, executive officers and other affiliated parties. The following paragraphs summarize certain information concerning certain transactions and relationships that have occurred during the past fiscal year or are currently proposed.

Paul Simon, Jr., a director of the Company, is a Member of the law firm Sauerwein, Simon & Blanchard, P.C., which had provided legal services to the Company in prior years.

Beginning in 2009, the Company provided advances to partially cover for months with no payroll, to two employees – Ed Hennessey and Mike Kime (who resigned from the Company in June 2010). As of December 31, 2011, the aggregate balance of advances totaled approximately $30,000.

Three members of our Board of Directors, Dr. Jackson Nickerson, Mr. Jose Bared, Sr. and Mr. David Bransby are parties to investments in our Convertible Note offerings – approximately $650,000 in the aggregate, including principal and interest as of December 31, 2011. Mr. Bared, Mr. Bransby and Dr. Nickerson have agreed to exchange all of their notes into our 11/10 Offering, except one for $50,000 for Dr. Nickerson. He has put the company on notice of his demand for payment and intent not to exchange this note. As of December 31, 2011, this note has not been repaid.

We use the Crane Agency Co. as our broker for business and property insurance. Our CEO’s brother was employed at the Crane Agency Co. through the end of 2010 and had been involved in the negotiation of our insurance policies. We continue to purchase insurance through the Crane Agency Co. and expect to continue in the future.

Determination of Director Independence

Rules of The NASDAQ Stock Market LLC (“Nasdaq”) require that a majority of the Board of Directors be “independent,” as defined in Nasdaq Marketplace Rule 5605(a)(2). Under the Nasdaq rules, the Board of Directors must make an affirmative determination that a director is independent by determining that the director has no relationships that, in the opinion of the Board of Directors, would interfere with the exercise of independent judgment in carrying out the responsibilities of a director. The Board of Directors has reviewed the independence of its directors under the Nasdaq rules. During this review, the Board of Directors considered transactions and relationships between each director or any member of his family and the Company. The Board of Directors has determined that Messrs. Nickerson, Bransby and Bared are independent under Nasdaq Rule 5605(a)(2).

ITEM 14. PRINCIPAL ACCOUNTANT FEES AND SERVICES

The following table sets forth the amount of audit fees, tax fees, audit-related fees and all other fees billed or expected to be billed by Milhouse & Neal, LLP, the Company’s independent registered public accounting firm and/or Larry O’Donnell, CPA (the Company’s former independent registered public accounting firm),:

	For the years ended December 31,
	2011		2010
Audit Fees (1)	$	10,200	$	18,900
Tax Fees		-		-
Audit-Related Fees		-		-
All Other Fees		-		-
Total Fees	$	10,200	$	18,900

(1)

Includes annual financial statement audit. For 2010, fees also include re-audits of our 2008 and 2009 Financial Statements. See our Form 8-K filed on October 27, 2010 and our Form 8-K/A filed on January 5, 2011 for further information on the change in the Independent Registered Public Accounting Firm, effective October 27, 2010.

PART IV

ITEM 15. EXHIBITS, FINANCIAL STATEMENT SCHEDULES

(a)	The following documents are filed as part of this report:

1.	Financial Statements:

Report of Independent Registered Public Accounting Firm

Consolidated Balance Sheets as of December 31, 2011 and 2010

Consolidated Statements of Operations for the years ended December 31, 2011, 2010 and 2009 and Inception to December 31, 2011

Consolidated Statements of Changes in Stockholders Equity for the years ended December 31, 2011, 2010 and 2009

Consolidated Statements of Cash Flows for the years ended December 31, 2011, 2010 and 2009 and Inception to December 31, 2011

Notes to Consolidated Financial Statements

Exhibits:

Exhibit Number		Description
2.1		Agreement and Plan of Merger and Reorganization by and among Cleantech Biofuels, Inc., Biomass NA Acquisition Subsidiary, Inc. and Biomass North America Licensing, Inc. dated as of July 14, 2008 (incorporated herein by reference to Exhibit 2.1 of the Registrant’s quarterly report on Form 10-Q for the period ended June 30, 2008).
3.1		Restated Certificate of Incorporation (incorporated herein by reference to Exhibit 3.1 of the Registrant’s registration statement on Form SB-2 filed on September 10, 2007, File No. 333-145939).
3.2		Restated By-Laws (incorporated herein by reference to Exhibit 3.2 of the Registrant’s registration statement on Form SB-2 filed on September 10, 2007, File No. 333-145939).
4.1		Form of Series A Convertible Debenture (incorporated herein by reference to Exhibit 4.1 of the Registrant’s registration statement on Form SB-2 filed on September 10, 2007, File No. 333-145939).
4.2		Investors’ Rights Agreement dated as of April 16, 2007 by and among SRS Energy, Inc. and certain Investors (incorporated herein by reference to Exhibit 4.2 of the Registrant’s registration statement on Form SB-2 filed on September 10, 2007, File No. 333-145939).
4.3		Series A Debenture Purchase Agreement dated as of April 16, 2007 by and among SRS Energy, Inc. and certain Investors (incorporated herein by reference to Exhibit 4.3 of the Registrant’s registration statement on Form SB-2 filed on September 10, 2007, File No. 333-145939).
10.1		Technology License Agreement between Bio Products International, Inc. and SRS Energy, Inc. dated as of March 8, 2007 (incorporated herein by reference to Exhibit 10.4 of the Registrant’s registration statement on Form SB-2 filed on September 10, 2007, File No. 333-145939).
10.4*		2007 Stock Option Plan (incorporated herein by reference to Exhibit 10.7 of the Registrant’s registration statement on Form SB-2 filed on September 10, 2007, File No. 333-145939).
10.5*		Form of Director Stock Option Agreement (incorporated herein by reference to Exhibit 10.8 of the Registrant’s registration statement on Form SB-2 filed on September 10, 2007, File No. 333-145939).
10.6*		Director Stock Purchase Agreement (incorporated herein by reference to Exhibit 10.9 of the Registrant’s registration statement on Form SB-2 filed on September 10, 2007, File No. 333-145939).
10.7*		Employment Agreement – Edward P. Hennessey, Jr. (incorporated herein by reference to Exhibit 10.10 of the Registrant’s registration statement on Form SB-2 filed on September 10, 2007, File No. 333-145939).
10.8*		Form of Employee Agreement – Tom Jennewein (incorporated herein by reference to Exhibit 10.11 of the Registrant’s registration statement on Form SB-2 filed on September 10, 2007, File No. 333-145939).
10.9*		Form of Employee Stock Option Agreement – Tom Jennewein (incorporated herein by reference to Exhibit 10.12 of the Registrant’s registration statement on Form SB-2 filed on September 10, 2007, File No. 333-145939).
10.10		Commercial Lease with Pershing Properties, LLC dated October 12, 2007 (incorporated herein by reference to Exhibit 10.13 of the Registrant’s registration statement on Form SB-2/A filed on November 30, 2007, File No. 333-145939).

10.11		Sublicense Agreement with HFTA dated March 20, 2008 (incorporated herein by reference to Exhibit 10.1 of the Registrant’s current report on Form 8-K filed March 25, 2008).
10.12		Sublicense Agreement among SRS Energy, Inc., Cleantech Biofuels, Inc. and HFTA for Methods and Apparatus for Treating Biomass Material (incorporated herein by reference to Exhibit 10.1 of the Registrant’s current report on Form 8-K filed on March 25, 2008).
10.13		Patent Purchase Agreement dated October 22, 2008 by and between Cleantech Biofuels, Inc. and World Waste Technologies, Inc. (incorporated herein by reference to Exhibit 10.15 of the Registrant’s current report on Form 8-K filed on October 27, 2008).
10.14		Note issued in favor of World Waste Technologies, Inc. dated October 22, 2008 (incorporated herein by reference to Exhibit 10.16 of the Registrant’s current report on Form 8-K filed on October 27, 2008).
10.15		Security Agreement between Cleantech Biofuels, Inc. and World Waste Technologies, Inc. dated October 22, 2008 (incorporated herein by reference to Exhibit 10.17 of the Registrant’s current report on Form 8-K filed on October 27, 2008).
10.16		Technology License and Joint Development Agreement among Biomass North America Licensing, Inc., Biomass North America, LLC and Anthony P. Noll (incorporated herein by reference to Exhibit 10.18 of the Registrant’s quarterly report on Form 10-Q for the period ended September 30, 2008).
10.17*		Form of employee stock purchase agreement entered into with Edward P. Hennessey, Jr., Mike Kime and Tom Jennewein (incorporated herein by reference to Exhibit 10.20 of the Registrant’s annual report on Form 10-K for the period ended December 31, 2008).
10.18		Amendment to Note and Warrant Exchange Agreement between Vertex Energy, Inc. and Cleantech Biofuels, Inc. dated July 23, 2009 (incorporated herein by reference to Exhibit 10.21 of the Registrant’s quarterly report on Form 10-Q for the period ended September 30, 2009).
10.19		Engagement Agreement between Cleantech Biofuels, Inc. and Houlihan Smith & Company dated June 30, 2010 (incorporated herein by reference to Exhibit 10.19 of the Registrant’s current report on Form 8-K filed on July 7, 2010). Subsequently terminated this agreement and the May 2011 amended agreement with Houlihan Capital, LLC effective Februray 9, 2012 (incorporated herein by reference to the Registrant’s current report on Form 8-K filed on February 15, 2012).
10.20		Promissory Note issued in favor of CMS Acquisition, LLC dated September 1, 2010 (incorporate herein by reference to Exhibit 10.20 of the Registrant’s current report on Form 8-K filed on September 8, 2010).
10.21		Security Agreement between Cleantech Biofuels, Inc. and CMS Acquisition, LLC dated September 1, 2010 (incorporated herein by reference to Exhibit 10.21 of the Registrant’s current report on Form 8-K filed on September 8, 2010).
10.22		Amendment dated February 11, 2011 to a Promissory Note issued in favor of CMS Acquisition, LLC dated September 1, 2010 (incorporated herein by reference to Exhibit 10.22 of the Registrant’s current report on Form 8-K filed on February 16, 2011).
10.23		Amendment No. 2 dated May 31, 2011 to a Promissory Note issued in favor of CMS Acquisition, LLC dated September 1, 2010 (incorporated herein by reference to Exhibit 10.23 of the Registrant’s current report on Form 8-K filed on June 1, 2011).
10.24		Amendment No. 3 dated July 29, 2011 to a Promissory Note issued in favor of CMS Acquisition, LLC dated September 1, 2010 (incorporated herein by reference to Exhibit 10.24 of the Registrant’s current report on Form 8-K filed on August 2, 2011).
10.25*		Form of Employee Stock Option Agreement entered into with Edward P. Hennessey, Jr. and Tom Jennewein (incorporated herein by reference to Exhibit 10.25 of the Registrant’s current report on Form 8-K filed on August 31, 2011).
10.26*		Form of Director Stock Option Agreement (incorporated herein by reference to Exhibit 10.26 of the Registrant’s current report on Form 8-K filed on October 19, 2011).
10.27		Amendment No. 4 dated November 7, 2011 to a Promissory Note issued in favor of CMS Acquisition, LLC dated September 1, 2010 (incorporated herein by reference to Exhibit 10.27 of the Registrant’s current report on Form 8-K filed on November 10, 2011).
10.28		Amendment No. 5 dated March 27, 2012 to a Promissory Note issued in favor of CMS Acquisition, LLC dated September 1, 2010.
14		Code of Ethics (incorporated herein by reference to Exhibit 14 of the Registrant’s annual report on Form 10-KSB for the period ended December 31, 2007).
21.1		List of Subsidiaries.
31.1		Certification of Chief Executive Officer pursuant to Rule 13a-14(a) and Rule 15d-14(a) of the Securities Exchange Act, as amended
31.2		Certification of principal financial officer pursuant to Rule 13a-14(a) and Rule 15d-14(a) of the Securities Exchange Act, as amended
32.1		Certificate (Pursuant to 18 U.S.C. Section 1350 as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002) of Chief Executive Officer
32.2		Certificate (Pursuant to 18 U.S.C. Section 1350 as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002) of principal financial officer

__________

*Management contract or compensatory plan or arrangement.

SIGNATURES

Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the Registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized.

	CleanTech Biofuels, Inc.
	(registrant)

March 29, 2012	By:	/s/ Edward P. Hennessey, Jr.
		Edward P. Hennessey, Jr.
		Chief Executive Officer

March 29, 2012	By:	/s/ Thomas G. Jennewein
		Thomas G. Jennewein
		Chief Financial Officer

Pursuant to the requirements of the Securities Exchange Act of 1934, this report has been signed below by the following persons on behalf of the Registrant and in the capacities and on the dates indicated.

March 29, 2012	By:	/s/ Edward P. Hennessey, Jr.
		Edward P. Hennessey, Jr., Chairman of the Board of Directors and Chief Executive Officer (principal executive officer)

March 29, 2012	By:	/s/ Thomas G. Jennewein
		Thomas G. Jennewein,
		Chief Financial Officer (principal financial and accounting officer)

March 29, 2012	By:	/ s/ Dr. Jackson Nickerson
		Jackson Nickerson, Director

March 29, 2012	By:	/s/ Dr. David Bransby
		David Bransby, Director

March 29, 2012	By:	/s/ Paul Simon, Jr.
		Paul Simon, Jr., Director

March 29, 2012	By:	/s/ Jose Bared, Sr.
		Jose Bared, Sr.., Director

INDEX TO EXHIBITS

Exhibit Number		Description
2.1		Agreement and Plan of Merger and Reorganization by and among Cleantech Biofuels, Inc., Biomass NA Acquisition Subsidiary, Inc. and Biomass North America Licensing, Inc. dated as of July 14, 2008 (incorporated herein by reference to Exhibit 2.1 of the Registrant’s quarterly report on Form 10-Q for the period ended June 30, 2008).
3.1		Restated Certificate of Incorporation (incorporated herein by reference to Exhibit 3.1 of the Registrant’s registration statement on Form SB-2 filed on September 10, 2007, File No. 333-145939).
3.2		Restated By-Laws (incorporated herein by reference to Exhibit 3.2 of the Registrant’s registration statement on Form SB-2 filed on September 10, 2007, File No. 333-145939).
4.1		Form of Series A Convertible Debenture (incorporated herein by reference to Exhibit 4.1 of the Registrant’s registration statement on Form SB-2 filed on September 10, 2007, File No. 333-145939).
4.2		Investors’ Rights Agreement dated as of April 16, 2007 by and among SRS Energy, Inc. and certain Investors (incorporated herein by reference to Exhibit 4.2 of the Registrant’s registration statement on Form SB-2 filed on September 10, 2007, File No. 333-145939).
4.3		Series A Debenture Purchase Agreement dated as of April 16, 2007 by and among SRS Energy, Inc. and certain Investors (incorporated herein by reference to Exhibit 4.3 of the Registrant’s registration statement on Form SB-2 filed on September 10, 2007, File No. 333-145939).
10.1		Technology License Agreement between Bio Products International, Inc. and SRS Energy, Inc. dated as of March 8, 2007 (incorporated herein by reference to Exhibit 10.4 of the Registrant’s registration statement on Form SB-2 filed on September 10, 2007, File No. 333-145939).
10.4*		2007 Stock Option Plan (incorporated herein by reference to Exhibit 10.7 of the Registrant’s registration statement on Form SB-2 filed on September 10, 2007, File No. 333-145939).
10.5*		Form of Director Stock Option Agreement (incorporated herein by reference to Exhibit 10.8 of the Registrant’s registration statement on Form SB-2 filed on September 10, 2007, File No. 333-145939).
10.6*		Director Stock Purchase Agreement (incorporated herein by reference to Exhibit 10.9 of the Registrant’s registration statement on Form SB-2 filed on September 10, 2007, File No. 333-145939).
10.7*		Employment Agreement – Edward P. Hennessey, Jr. (incorporated herein by reference to Exhibit 10.10 of the Registrant’s registration statement on Form SB-2 filed on September 10, 2007, File No. 333-145939).
10.8*		Form of Employee Agreement – Tom Jennewein (incorporated herein by reference to Exhibit 10.11 of the Registrant’s registration statement on Form SB-2 filed on September 10, 2007, File No. 333-145939).
10.9*		Form of Employee Stock Option Agreement – Tom Jennewein (incorporated herein by reference to Exhibit 10.12 of the Registrant’s registration statement on Form SB-2 filed on September 10, 2007, File No. 333-145939).
10.10		Commercial Lease with Pershing Properties, LLC dated October 12, 2007 (incorporated herein by reference to Exhibit 10.13 of the Registrant’s registration statement on Form SB-2/A filed on November 30, 2007, File No. 333-145939).
10.11		Sublicense Agreement with HFTA dated March 20, 2008 (incorporated herein by reference to Exhibit 10.1 of the Registrant’s current report on Form 8-K filed March 25, 2008).
10.12		Sublicense Agreement among SRS Energy, Inc., Cleantech Biofuels, Inc. and HFTA for Methods and Apparatus for Treating Biomass Material (incorporated herein by reference to Exhibit 10.1 of the Registrant’s current report on Form 8-K filed on March 25, 2008).
10.13		Patent Purchase Agreement dated October 22, 2008 by and between Cleantech Biofuels, Inc. and World Waste Technologies, Inc. (incorporated herein by reference to Exhibit 10.15 of the Registrant’s current report on Form 8-K filed on October 27, 2008).
10.14		Note issued in favor of World Waste Technologies, Inc. dated October 22, 2008 (incorporated herein by reference to Exhibit 10.16 of the Registrant’s current report on Form 8-K filed on October 27, 2008).
10.15		Security Agreement between Cleantech Biofuels, Inc. and World Waste Technologies, Inc. dated October 22, 2008 (incorporated herein by reference to Exhibit 10.17 of the Registrant’s current report on Form 8-K filed on October 27, 2008).
10.16		Technology License and Joint Development Agreement among Biomass North America Licensing, Inc., Biomass North America, LLC and Anthony P. Noll (incorporated herein by reference to Exhibit 10.18 of the Registrant’s quarterly report on Form 10-Q for the period ended September 30, 2008).
10.17*		Form of employee stock purchase agreement entered into with Edward P. Hennessey, Jr., Mike Kime and Tom Jennewein (incorporated herein by reference to Exhibit 10.20 of the Registrant’s annual report on Form 10-K for the period ended December 31, 2008).

10.18		Amendment to Note and Warrant Exchange Agreement between Vertex Energy, Inc. and Cleantech Biofuels, Inc. dated July 23, 2009 (incorporated herein by reference to Exhibit 10.21 of the Registrant’s quarterly report on Form 10-Q for the period ended September 30, 2009).
10.19		Engagement Agreement between Cleantech Biofuels, Inc. and Houlihan Smith & Company dated June 30, 2010 (incorporated herein by reference to Exhibit 10.19 of the Registrant’s current report on Form 8-K filed on July 7, 2010). Subsequently terminated this agreement and the May 2011 amended agreement with Houlihan Capital, LLC effective Februray 9, 2012 (incorporated herein by reference to the Registrant’s current report on Form 8-K filed on February 15, 2012).
10.20		Promissory Note issued in favor of CMS Acquisition, LLC dated September 1, 2010 (incorporate herein by reference to Exhibit 10.20 of the Registrant’s current report on Form 8-K filed on September 8, 2010).
10.21		Security Agreement between Cleantech Biofuels, Inc. and CMS Acquisition, LLC dated September 1, 2010 (incorporated herein by reference to Exhibit 10.21 of the Registrant’s current report on Form 8-K filed on September 8, 2010).
10.22		Amendment dated February 11, 2011 to a Promissory Note issued in favor of CMS Acquisition, LLC dated September 1, 2010 (incorporated herein by reference to Exhibit 10.22 of the Registrant’s current report on Form 8-K filed on February 16, 2011).
10.23		Amendment No. 2 dated May 31, 2011 to a Promissory Note issued in favor of CMS Acquisition, LLC dated September 1, 2010 (incorporated herein by reference to Exhibit 10.23 of the Registrant’s current report on Form 8-K filed on June 1, 2011).
10.24		Amendment No. 3 dated July 29, 2011 to a Promissory Note issued in favor of CMS Acquisition, LLC dated September 1, 2010 (incorporated herein by reference to Exhibit 10.24 of the Registrant’s current report on Form 8-K filed on August 2, 2011).
10.25*		Form of Employee Stock Option Agreement entered into with Edward P. Hennessey, Jr. and Tom Jennewein (incorporated herein by reference to Exhibit 10.25 of the Registrant’s current report on Form 8-K filed on August 31, 2011).
10.26*		Form of Director Stock Option Agreement (incorporated herein by reference to Exhibit 10.26 of the Registrant’s current report on Form 8-K filed on October 19, 2011).
10.27		Amendment No. 4 dated November 7, 2011 to a Promissory Note issued in favor of CMS Acquisition, LLC dated September 1, 2010 (incorporated herein by reference to Exhibit 10.27 of the Registrant’s current report on Form 8-K filed on November 10, 2011).
10.28		Amendment No. 5 dated March 27, 2012 to a Promissory Note issued in favor of CMS Acquisition, LLC dated September 1, 2010.
14		Code of Ethics (incorporated herein by reference to Exhibit 14 of the Registrant’s annual report on Form 10-KSB for the period ended December 31, 2007).
21.1		List of Subsidiaries.
31.1		Certification of Chief Executive Officer pursuant to Rule 13a-14(a) and Rule 15d-14(a) of the Securities Exchange Act, as amended
31.2		Certification of principal financial officer pursuant to Rule 13a-14(a) and Rule 15d-14(a) of the Securities Exchange Act, as amended
32.1		Certificate (Pursuant to 18 U.S.C. Section 1350 as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002) of Chief Executive Officer
32.2		Certificate (Pursuant to 18 U.S.C. Section 1350 as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002) of principal financial officer

____________

*Management contract or compensatory plan or arrangement.

Exhibit 10.28

AMENDMENT No. 5 TO PROMISSORY NOTE

This Amendment No. 5 to the Promissory Note, originally dated September 1, 2010 (the “Note”), previously amended February 11, 2011, May 31, 2011, July 29, 2011 and November 7, 2011 (the “Amendments”), is entered into as of the 27th day of March, 2012, by and between CMS Acquisition, LLC (“CMS”) and CleanTech Biofuels, Inc. (“CTB”).

WHEREAS, the Note is secured by the CTB owned U.S. Patent No. 6,306,248 pursuant to a Security Agreement dated as of September 1, 2010, between CMS and CTB (the “Security Agreement”);

WHEREAS, a payment of $25,000 was made on February 11, 2011 for interest to date and principal, by CTB on the Note;

WHEREAS, as of May 16, 2011, the rate to accrue interest increased to 10.0% per annum (from 9.0% per annum);

WHEREAS, as of November 7, 2011, Warrant A1 issued with the original Note on September 1, 2010 was re-dated to November 7, 2011; and

WHEREAS, the parties wish to amend the terms of the Note as set forth below.

NOW THEREFORE, the parties hereto agree as follows:

1.	The Maturity Date, as defined in the Amendments, shall be changed to May 15, 2012 from February 7, 2012.

2.	All remaining terms and conditions of the Note, Security Agreement and Warrant shall continue in full force and effect.

IN WITNESS WHEREOF, CTB and CMS have caused this Amendment No. 5 to the Note to be executed and delivered by their duly authorized officers as of the day and year set forth above.

CLEANTECH BIOFUELS, INC.:	By:	/s/
		Name: Edward P. Hennessey
		Title: CEO

CMS Acquisition, LLC:	By:	/s/
		Name:
		Title:

Exhibit 21.1

List of Subsidiaries

SRS Energy, Inc., a Delaware corporation

CTB Licensing LLC

Exhibit 31.1

Certification of Chief Executive Officer pursuant to Rule 13a-14(a) and Rule 15d-14(a) of the Securities Exchange Act, as amended

I, Edward P. Hennessey, Jr., certify that:

1. I have reviewed this Annual Report of CleanTech Biofuels, Inc.;

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrant's other certifying officer(s) and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a–15(e) and 15d–15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a–15(f) and 15d–15(f)) for the registrant and have:

(a) Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

(b) Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

(c) Evaluated the effectiveness of the registrant's disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

(d) Disclosed in this report any change in the registrant's internal control over financial reporting that occurred during the registrant's most recent fiscal quarter (the registrant's fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant's internal control over financial reporting; and

5. The registrant's other certifying officer(s) and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant's auditors and the audit committee of the registrant's board of directors (or persons performing the equivalent functions):

(a) All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant's ability to record, process, summarize and report financial information; and

(b) Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant's internal control over financial reporting.

Date: March 29, 2012	By:	/s/ Edward P. Hennessey, Jr.
		Edward P. Hennessey, Jr.
		Chief Executive Officer

Exhibit 31.2

Certification of Chief Financial Officer pursuant to Rule 13a-14(a) and Rule 15d-14(a) of the Securities Exchange Act, as amended

I, Thomas G. Jennewein, certify that:

1. I have reviewed this Annual Report of CleanTech Biofuels, Inc.;

(b) Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant's internal control over financial reporting.

Date: March 29, 2012	By:	/s/ Thomas G. Jennewein
		Thomas G. Jennewein
		Chief Financial Officer

Exhibit 32.1

Certificate (Pursuant to 18 U.S.C. Section 1350 as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002) of Chief Executive Officer

I, Edward P. Hennessey, Jr., Chief Executive Officer of CleanTech Biofuels, Inc. (the “Company”), do hereby certify, pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, that, to my knowledge:

1.	This Annual Report on Form 10-K of the Company for the year ended December 31, 2011 as filed with the Securities and Exchange Commission (the “report”), fully complies with the requirements of Section 13(a) or 15(d) of the Securities Exchange Act of 1934; and

2.	The information contained in the report fairly presents, in all material respects, the financial condition and results of operations of the Company.

Date: March 29, 2012	By:	/s/ Edward P. Hennessey, Jr.
		Edward P. Hennessey, Jr.
		Chief Executive Officer

Exhibit 32.2

Certificate (Pursuant to 18 U.S.C. Section 1350 as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002) of principal financial officer

I, Thomas G. Jennewein, Chief Financial Officer of CleanTech Biofuels, Inc. (the “Company”), do hereby certify, pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, that, to my knowledge:

1. This Annual Report on Form 10-K of the Company for the year ended December 31, 2011 as filed with the Securities and Exchange Commission (the “report”), fully complies with the requirements of Section 13(a) or 15(d) of the Securities Exchange Act of 1934; and

2. The information contained in the report fairly presents, in all material respects, the financial condition and results of operations of the Company.

Date: March 29, 2012	By:	/s/ Thomas G. Jennewein
		Thomas G. Jennewein
		Chief Financial Officer