Exhibit 10.1

AMENDMENT NO. 1 TO SALES AGREEMENT

August 25, 2015

Cowen and Company, LLC

599 Lexington Avenue

New York, NY 10022

Ladies and Gentlemen:

EnteroMedics Inc., a Delaware corporation (the “ Company ”), and Cowen and Company, LLC (“ Cowen ”), are parties to that certain Sales Agreement dated June 13, 2014 (the “ Original Agreement ”). All capitalized terms not defined herein shall have the meanings ascribed to them in the Original Agreement. The parties, intending to be legally bound, hereby amend the Original Agreement as follows:

1. Section 1 of the Original Agreement is hereby deleted and replaced with the following:

“ Issuance and Sale of Shares . The Company agrees that, from time to time during the term of this Agreement, on the terms and subject to the conditions set forth herein, it may issue and sell through Cowen, acting as agent and/or principal, shares of the Company’s common stock, par value $0.01 per share (the “ Common Stock ”) having an aggregate offering price of up to $25,000,000 by any method permitted by law deemed to be an “at the market offering” as defined in Rule 415 of the Securities Act (as defined below). Notwithstanding anything to the contrary contained herein, the parties hereto agree that compliance with the limitation set forth in this Section 1 on the number of shares of Common Stock issued and sold under this Agreement shall be the sole responsibility of the Company, and Cowen shall have no obligation in connection with such compliance. Pursuant to this Agreement, shares of our common stock were previously sold for $7,579,013 in aggregate gross proceeds under a separate prospectus supplement. Under this Agreement, as amended by Amendment No. 1 to Sales Agreement, the Company, through Cowen, may offer and sell further shares of common stock having an aggregate offering price of up to $17,420,987 pursuant to the Prospectus (as defined below). The issuance and sale of Common Stock through Cowen will be effected pursuant to the Registration Statement (as defined below) filed by the Company and declared effective by the Securities and Exchange Commission (the “ Commission ”), although nothing in this Agreement shall be construed as requiring the Company to use the Registration Statement (as defined below) to issue the Common Stock.

The Company has filed, in accordance with the provisions of the Securities Act of 1933, as amended, and the rules and regulations thereunder (collectively, the “ Securities Act ”), with the Commission a registration statement on Form S-3 (File No. 333- 195855), including a base prospectus, relating to certain securities, including the Common Stock, to be issued from time to time by the Company, and which incorporates by reference documents that the Company has filed or will file in accordance with the provisions of the

Securities Exchange Act of 1934, as amended, and the rules and regulations thereunder (collectively, the “ Exchange Act ”). The Company has prepared a prospectus supplement specifically relating to the Common Stock being offered under this Agreement (the “ Prospectus Supplement ”) to the base prospectus included as part of such registration statement. The Company has furnished to Cowen, for use by Cowen, copies of the prospectus included as part of such registration statement, as supplemented by the Prospectus Supplement, relating to the Common Stock. Except where the context otherwise requires, such registration statement, as amended when it became effective, including all documents filed as part thereof or incorporated by reference therein, and including any information contained in a Prospectus (as defined below) subsequently filed with the Commission pursuant to Rule 424(b) under the Securities Act or deemed to be a part of such registration statement pursuant to Rule 430B or 462(b) of the Securities Act, is herein called the “ Registration Statement . ” The base prospectus, including all documents incorporated therein by reference, included in the Registration Statement, as it may be supplemented by the Prospectus Supplement, in the form in which such prospectus and/or Prospectus Supplement have most recently been filed by the Company with the Commission pursuant to Rule 424(b) under the Securities Act, together with any “issuer free writing prospectus,” as defined in Rule 433 of the Securities Act Regulations (“Rule 433”), relating to the Common Stock offered under this Agreement that (i) is required to be filed with the Commission by the Company or (ii) is exempt from filing pursuant to Rule 433(d)(5)(i), in each case in the form filed or required to be filed with the Commission or, if not required to be filed, in the form retained in the Company’s records pursuant to Rule 433(g), is herein called the “ Prospectus .” Any reference herein to the Registration Statement, the Prospectus or any amendment or supplement thereto shall be deemed to refer to and include the documents incorporated by reference therein, and any reference herein to the terms “amend,” “amendment” or “supplement” with respect to the Registration Statement or the Prospectus shall be deemed to refer to and include the filing after the execution hereof of any document with the Commission deemed to be incorporated by reference therein. For purposes of this Agreement, all references to the Registration Statement, the Prospectus or to any amendment or supplement thereto shall be deemed to include any copy filed with the Commission pursuant to either the Electronic Data Gathering Analysis and Retrieval System or Interactive Data Electronic Applications (collectively “ IDEA ”).

2. In Section 6 of the Original Agreement, clause (gg) is deleted and replaced with the words “Intentionally omitted.”

3. All references to “June 13, 2014” set forth in Schedule 1 and Exhibit 7(l) of the Original Agreement are revised to read “June 13, 2014 (as amended by Amendment No. 1 to Sales Agreement, dated August 25, 2015)”.

4. Except as specifically set forth herein, all other provisions of the Original Agreement shall remain in full force and effect.

5. Entire Agreement; Amendment; Severability . This Amendment No. 1 together with the Original Agreement (including all schedules and exhibits attached hereto and thereto

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and Placement Notices issued pursuant hereto and thereto) constitutes the entire agreement and supersedes all other prior and contemporaneous agreements and undertakings, both written and oral, among the parties hereto with regard to the subject matter hereof. All references in the Original Agreement to the “Agreement” shall mean the Original Agreement as amended by this Amendment No. 1; provided, however , that all references to “date of this Agreement” in the Original Agreement shall continue to refer to the date of the Original Agreement, and the reference to “time of execution of this Agreement” set forth in Section 13(a) shall continue to refer to the time of execution of the Original Agreement.

6. Applicable Law; Consent to Jurisdiction . This amendment shall be governed by, and construed in accordance with, the internal laws of the State of New York without regard to the principles of conflicts of laws. Each party hereby irrevocably submits to the non-exclusive jurisdiction of the state and federal courts sitting in the City of New York, borough of Manhattan, for the adjudication of any dispute hereunder or in connection with any transaction contemplated hereby, and hereby irrevocably waives, and agrees not to assert in any suit, action or proceeding, any claim that it is not personally subject to the jurisdiction of any such court, that such suit, action or proceeding is brought in an inconvenient forum or that the venue of such suit, action or proceeding is improper. Each party hereby irrevocably waives personal service of process and consents to process being served in any such suit, action or proceeding by mailing a copy thereof (certified or registered mail, return receipt requested) to such party at the address in effect for notices to it under this amendment and agrees that such service shall constitute good and sufficient service of process and notice thereof. Nothing contained herein shall be deemed to limit in any way any right to serve process in any manner permitted by law.

7. Waiver of Jury Trial . The Company and Cowen each hereby irrevocably waives any right it may have to a trial by jury in respect of any claim based upon or arising out of this amendment or any transaction contemplated hereby.

8. Counterparts . This amendment may be executed in two or more counterparts, each of which shall be deemed an original, but all of which together shall constitute one and the same instrument. Delivery of an executed amendment by one party to the other may be made by facsimile transmission.

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If the foregoing correctly sets forth the understanding among the Company and Cowen, please so indicate in the space provided below for that purpose, whereupon this letter shall constitute a binding amendment to the Agreement between the Company and Cowen.

Exhibit 10.2

FIRST AMENDMENT TO LEASE

This First Amendment to Lease (“First Amendment”) is made and entered into this 20th day of August, 2015, by and between ROSEVILLE PROPERTIES MANAGEMENT COMPANY, INC. , a Minnesota corporation, as agent for COMMERS-KLODT III, a Minnesota general partnership (“Landlord”), and ENTEROMEDICS INC., a Delaware corporation (“Tenant”).

RECITALS

WHEREAS, Landlord and Tenant entered into a certain Commercial Lease, dated October 1, 2008, (“Original Lease”), pertaining to approximately 28,388 square feet of space at the property located at 2800 Patton Road, Roseville, Minnesota 55113 (“Demised Premises”) attached on Exhibit A.

WHEREAS, Landlord and Tenant wish to amend and modify the Lease in order to, among other things, extend the Term of the Lease (and provide Tenant with a renewal option), modify the amount of Base Rent, and provide for repair, replacement and maintenance of HVAC rooftop units which will be passed through to Tenant as outlined in paragraph 9, all of which modifications will be upon the terms and conditions hereinafter set forth.

NOW, THEREFORE, in consideration of the premises and other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the parties hereby agree as follows:

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“ 38.0 OPTION TO RENEW:

Tenant shall have a one (1) time right to renew the term of this Lease for one (1) period of three (3) years (the “Renewal Term”), subject to the following terms and conditions:

a. Tenant shall not be in default in the performance of any of the terms, covenants, or conditions of this Lease, either at the time of the exercise of the right to renew or at the time of the commencement of the Renewal Term.

b. Base Rent during the Renewal Term shall be the Fair Market Rent (as defined below). Tenant may request from Landlord, not more than two hundred seventy (270) days prior to the expiration of the Extension Term, Landlord’s determination of “Fair Market Rent” (as defined below).

c. For purposes of this Article, “Fair Market Rent” means the annual Base Rent that a tenant would pay to a landlord under a net lease containing other terms and conditions substantially as set forth herein with respect to comparable premises in a comparable building in the general geographic area that the Demised Premises are located where both the landlord and tenant are willing and able to enter into such a lease transaction but neither would be under any compulsion to do so, and taking into account all relevant facts and circumstances concerning the Building, the parties and the relevant market (i.e., rental concessions, leasehold improvement allowances, and brokerage fees). In determining, for purposes of this Article 38.0, Fair Market Rent, Landlord shall give notice to Tenant of its determination of Fair Market Rent, after request by Tenant, within at least ten (10) days subsequent to such request, and such determination shall constitute Landlord’s determination of Fair Market Rent. In the event Tenant disagrees with Landlord’s determination of Fair Market Rent, Fair Market Rent shall be determined by the following methodology:

Both parties shall then have a period of sixty (60) days in which to reach a mutual agreement on Fair Market Rent for the Renewal Term. In the event the parties are unable to reach acceptable terms within this period, then this renewal option shall no longer be of any force or effect.

d. Tenant and Landlord shall agree on terms to renew the term of this Lease at least one hundred twenty (120) days prior to the expiration of the Extension Term. If Tenant fails to notify Landlord within such time and in the manner herein provided or Tenant and Landlord are unable to reach acceptable terms under the timeframes provided, Tenant’s right to renew the term of this Lease beyond the Extension Term shall expire and shall become null, void and of no further force or effect.

e. There shall be no further renewal rights after commencement of the Renewal Term unless agreed upon by the parties as part of these renewal discussions.

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f. The option to renew is not transferrable and shall be “personal” to Tenant and in no event will any assignee or sublessee have any rights to exercise any rights set forth herein unless such assignee or sublessee is a Tenant Affiliate or the result of a merger or acquisition in which case the Tenant is a wholly owned subsidiary.

“a. Tenant’s Right of First Offer is subject to and is conditioned upon (i) the Lease must be in full force and effect; (ii) Tenant shall not be in default herein; (iii) Tenant’s offer to lease the Offer Space must be for a term which is co-terminus with the Term of this Lease (as extended pursuant to the provisions set forth in Section 6 of this First Amendment) and have a remaining term of not less than three (3) years; and (iv) Tenant’s offer to lease the Offer Space must meet such other terms and conditions as are set forth in this Article.”

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IN WITNESS WHEREOF, the parties have executed this First Amendment to be effective as of the date first written above.

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EXHIBIT A

PREMISES

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Roseville Properties/C145

2800 Patton Road

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