Exhibit 99.1

FORM 51-102F3

MATERIAL CHANGE REPORT

AETERNA ZENTARIS INC.

Aeterna Zentaris Inc. (the “ Corporation ”)

1405 du Parc-Technologique Boulevard

Quebec City, Québec

Canada, G1P 4P5

October 2, 2012.

On October 3, 2012, the Corporation issued a news release indicating the material change, which was disseminated in Canada on the Canada NewsWire service. A copy of such news release is attached hereto as Schedule A .

On October 3, 2012, the Corporation announced that the issued and outstanding common shares of the Corporation (“ Common Shares ”) have been consolidated (the “ Share Consolidation ”) on a six (6) to one (1) basis effective as of October 2, 2012 following the filing of Articles of Amendment and the receipt of a Certificate of Amendment in respect thereof.

On October 3, 2012, the Corporation announced that the issued and outstanding Common Shares have been consolidated on a six (6) to one (1) basis effective as of October 2, 2012 following the filing of Articles of Amendment and the receipt of a Certificate of Amendment in respect thereof.

The news release attached as Schedule A hereto sets forth a complete description of the Share Consolidation.

Not applicable.

Not applicable.

Further information regarding the matters described in this report may be obtained from Dennis Turpin, Senior Vice President and Chief Financial Officer. Mr. Turpin is knowledgeable about the details of the material change and may be contacted at (418) 652-8525.

October 3, 2012.

SCHEDULE A

NEWS RELEASE

(October 3, 2012)

Aeterna Zentaris Announces Share Consolidation to Regain

NASDAQ Compliance

Québec City, Canada, October 3, 2012 – Aeterna Zentaris Inc. (NASDAQ: AEZS) (TSX: AEZ) (the “Company”) today announced that the issued and outstanding common shares of the Company (“Common Shares”) have been consolidated (the “Consolidation”) on a six (6) to one (1) basis effective as of October 2, 2012. The purpose of the Consolidation is to enable the Company to attempt to regain compliance with the minimum bid price requirement of the NASDAQ Stock Market (“NASDAQ”).

The Company has received conditional approval from the Toronto Stock Exchange (“TSX”) to effect the Consolidation and has provided notification of the Consolidation to NASDAQ. Subject to final confirmation by TSX and NASDAQ, it is expected that the post-Consolidation Common Shares will begin trading on each of NASDAQ and TSX at the opening of markets on or about October 5, 2012 under its current NASDAQ and TSX trading symbols, “AEZS” and “AEZ”, respectively, under the new post-Consolidation CUSIP number of 007975303.

The Consolidation will reduce the number of outstanding Common Shares from approximately 112.4 million to approximately 18.7 million. Proportionate adjustments will be made to the Company’s outstanding warrants and stock options. No fractional Common Shares have been issued pursuant to the Consolidation and any fractional shares that would have otherwise been issued have been rounded down to the nearest whole number. Any and all such fractional shares will be aggregated and sold by the Company’s transfer agent and registrar on the market, with the net proceeds being proportionately distributed to shareholders.

Letters of transmittal with respect to the Consolidation are being mailed to the Company’s registered shareholders. All registered shareholders will be required to send their share certificates representing pre-Consolidation Common Shares, along with a properly executed letter of transmittal, to the Company’s registrar and transfer agent, Computershare Investor Services Inc., in accordance with the instructions provided in the letter of transmittal. All registered shareholders who submit to Computershare a completed letter of transmittal, along with their respective certificates representing pre-Consolidation Common Shares, will receive in exchange new certificates representing their post-Consolidation Common Shares. Shareholders who hold their Common Shares through a broker, investment dealer, bank, trust company or other nominee or intermediary should contact that nominee or intermediary for assistance in depositing their Common Shares in connection with the Share Consolidation.

About Aeterna Zentaris

Aeterna Zentaris is an oncology and endocrinology drug development company currently investigating treatments for various unmet medical needs. The Company’s pipeline encompasses compounds at all stages of development, from drug discovery through to marketed products. For more information please visit www.aezsinc.com .

Forward-Looking Statements

This press release contains forward-looking statements made pursuant to the safe harbour provisions of the U.S. Securities Litigation Reform Act of 1995. Forward-looking statements involve known and unknown risks and uncertainties that could cause the Company’s actual results to differ materially from those in the forward-looking statements. For example, because the market price of the Company’s Common Shares will also be based on the Company’s financial and operational results, its financial position, including its capital availabilities and liquidity resources, the development of its product pipeline, market conditions, the market perception of its business and other factors, which are unrelated to the number of shares outstanding, there can be no assurance that the market price of the Common Shares will in fact increase following the Consolidation or will not decrease in the future, or that the minimum closing bid price of the Common Shares will meet NASDAQ’s minimum bid price requirement. Further, there can be no assurance that the Consolidation alone will guarantee the continued listing of the Common Shares on The NASDAQ Global Market or that the Common Shares will not be delisted due to a failure to meet other NASDAQ continued listing requirements. Other such risks and uncertainties include, among others, the availability of funds and resources to pursue R&D projects, the successful and timely completion of clinical studies, the risk that safety and efficacy data from any of our Phase 3 trials may not coincide with the data analyses from previously reported Phase 1 and/or Phase 2 clinical trials, the ability of the Company to take advantage of business opportunities in the pharmaceutical industry, uncertainties related to the regulatory process and general changes in economic conditions. Investors should consult the Company’s quarterly and annual filings with the Canadian and U.S. securities commissions for additional information on risks and uncertainties relating to forward-looking statements. Investors are cautioned not to rely on these forward-looking statements. The Company does not undertake to update these forward-looking statements. We disclaim any obligation to update any such factors or to publicly announce the result of any revisions to any of the forward-looking statements contained herein to reflect future results, events or developments, unless required to do so by a governmental authority or by applicable law.

Investor Relations

Ginette Beaudet Vallières

Investor Relations Coordinator

(418) 652-8525 ext. 265

gvallieres@aezsinc.com

Media Relations

Paul Burroughs

Director of Communications

(418) 652-8525 ext. 406

pburroughs@aezsinc.com

– 2 –

Exhibit 99.2

Exhibit 99.2

Certificate of Amendment

Canada Business Corporations Act

Certificat de modification

Loi canadienne sur les sociétés par actions

AETERNA ZENTARIS INC.

Corporate name / Dénomination sociale

264271-9

Corporation number / Numéro de société

I HEREBY CERTIFY that the articles of the above-named corporation are amended under section 178 of the Canada Business Corporations Act as set out in the attached articles of amendment.

JE CERTIFIE que les statuts de la société susmentionnée sont modifiés aux termes de l’article 178 de la Loi canadienne sur les sociétés par actions, tel qu’il est indiqué dans les clauses modificatrices ci-jointes.

Marcie Girouard

Director / Directeur

2012-10-02

Date of Amendment (YYYY-MM-DD)

Date de modification (AAAA-MM-JJ)

Industry Canada

Industrie Canada

Corporation Canada

Corportione Canada

Form 4

Instructions

3 Any changes in the articles of the corporation must be made in accordance with section 27 or 177 of the CBCA.

A: If an amendment involves a change of corporate name (including the addition of the English or French version of the corporate name), the new name must comply with sections 10 and 12 of the CBCA as well as part 2 of the regulations, and the Articles of Amendment must be accompanied by a Canada-based NUANS® search report dated not more than nearby (90) days prior to the receipt of the articles by Corporations Canada. A numbered name may be assigned under subsection 11(2) of the CBCA without a NUANS® search.

D: Any other amendments must correspond to the paragraph and subparagraph referenced in the articles being amended. If the space available is insufficient, please attach a schedule to the form.

4. Declaration

This form must be signed by a director or an officer of the corporation (subsection 262(2) of the CBCA).

General

The information you provide in this document is collected under the authority of the CBCA and will be stored in personal information bank number IC/PPU-049. Personal information that you provide is protected under the provisions of the Privacy Act. However, public disclosure pursuant to section 266 of the CBCA is permitted under the Privacy Act.

If you require more information, please consult our website at www.corporationscanada.ic.gc.ca or contact us at 613-941-9042 (Ottawa region), toll-free at 1-666-333-5556 or by email at coorporatonscanada@ic.gc.ca.

Prescribed Fees

Corporations Canada Online Filling Centre: $200

By mail or fax: $200 paid by cheque payable to the Receiver General for Canada or by credit card (American Express® MasterCard® or Visa®).

Important Reminders

Changes of registered office address and/or mailing address:

Complete and the Change of Registered Office Address (Form 3):

Changes of directors or changes of a director’s address:

Complete and file changes Regarding Directors (Form 6):

These forms can be filed electronically, by mail or by fax free of charge.

File documents online:

Corporations Canada Online Filling Centre:

www.corporatinscanada.ic.gc.ca

or send documents by mail:

Director General,

Corporations Canada

Jean Edmonds Tower South

9th Floor

365 Laurier Ave. West

Ottawa ON K1a 0C8

By Facsimile:

613-941-0999

Articles of Amendment

(Section 27 or 177 of the Canada Business Corporations Act (CBCA)

1 Corporation name

AETERNA ZENTARIS INC.

2 Corporation number

264271_9

3 The articles are amended as follows:

(Please note that more than one section can be filled out)

A: The corporation changes its name to:

B: The corporation changes the province or territory in Canada where the registered office is situated to: (Do not indicate the full address)

C: The Corporation changes the minimum and/or maximum number of directors to: (For a fixed number of directors, please indicate the same number in both the minimum and maximum options)

Maximum: Medium:

D: Other changes: (e.g., to the classes of shares, to restrictions on share transfers, to restrictions on the businesses of the corporation or to any other provisions that are permitted by the CBCA to be set out in the Articles) Please specify.

The issued and outstanding common shares in the capital of the Corporation (each, a Common Share) are hereby consolidated on the basis of one (1) post-consolidation Common Share for each six (6) pre-consolidation Common Shares.

No fractional Common Shares shall be issued upon the consolidation of the issued and outstanding Common Shares in accordance with the foregoing. All new Common Shares to be issued upon the issuance of the Certificate of Amendment shall be rounded down to the nearest whole number of Common Shares and all fractional Common Shares to which a registered shareholder would otherwise become entitled as a result of the consolidation will be aggregated and sold by the Corporation’s transfer agent and registrar on the market, with the net proceeds therefrom being proportionately distributed to registered shareholders.

Declaration

I hereby certify that I am a director or an officer of the corporation.

Signature

First Name Telephone number

Note: Misrepresentation constitutes an offence and, an summary coincide, a person is liable to a fine not exceeding £5000 or to imprisonment for a term not exceeding six months or both (subsection 256(1) of the CBCA).

IC 3069 (2006/12)

Exhibit 99.3

LETTER OF TRANSMITTAL FOR REGISTERED HOLDERS OF COMMON SHARES OF

AETERNA ZENTARIS INC.

For use in connection with a share consolidation

This letter of transmittal (the Letter of Transmittal ) is for use by registered holders of common shares (the Common Shares ) of Aeterna Zentaris Inc. ( Aeterna Zentaris ) in connection with the consolidation of the Common Shares on the basis of one (1) new Common Share for every six (6) old Common Shares (the Share Consolidation ). The Share Consolidation was approved by the holders of Common Shares at Aeterna Zentaris’ special meeting of shareholders on August 15, 2012 (the Meeting ) and became effective on or about the date of mailing of this Letter of Transmittal.

Shareholders are referred to Aeterna Zentaris’ Notice of Special Meeting and Management Information Circular in connection with the Meeting, dated July 10, 2012 (the Circular ), for further information relating to the Share Consolidation. A copy of the Circular is available under the profile of Aeterna Zentaris at www.sedar.com .

Shareholders who hold their Common Shares through a broker, investment dealer, bank, trust company or other nominee or intermediary should contact that nominee or intermediary for assistance in depositing their Common Shares in connection with the Share Consolidation.

The undersigned hereby represents and warrants that he is the owner of the number of Common Shares indicated in the table below, which shares are represented by the share certificate(s) described below and delivered herewith and the undersigned has good title to the shares represented by the said certificate(s), free and clear of all liens, charges and encumbrances, and has full power and authority to herewith deposit such shares.

The above-listed share certificates are hereby surrendered in exchange for a new certificate representing Common Shares on the basis of one (1) new Common Share for every six (6) old Common Shares represented by the above-listed share certificates, in accordance with the Share Consolidation.

No fractional shares will be issued in connection with the Share Consolidation. If, as a result of the Share Consolidation, a shareholder becomes entitled to a fractional share, such fraction will be rounded down to the nearest whole number. Any and all such fractional shares will be aggregated and sold by Computershare Investor Services Inc. on the market, with the proceeds therefrom, after expenses and commissions, being proportionately distributed to registered shareholders.

The undersigned authorizes and directs Computershare Investor Services Inc. to issue the share certificates representing the number of new Common Shares to which the undersigned is entitled as a result of the Share Consolidation, as indicated below, and to mail such certificates to the address indicated below or, if no instructions are given, in the name and to the address of the undersigned as the same appears on the share register maintained by Aeterna Zentaris.

INSTRUCTIONS

If a share certificate has been lost or destroyed, the Letter of Transmittal must be completed as fully as possible and forwarded to Computershare Investor Services Inc. together with a letter stating the loss. Computershare Investor Services Inc. will contact you to advise of the replacement requirements.

By Mail:

P.O. Box 7021

31 Adelaide Street East

Toronto, Ontario

M5C 3H2

Attention: Corporate Actions

By Registered Mail, Hand or by Courier:

Toronto

100 University Avenue

9 ^th Floor

Toronto, Ontario

M5J 2Y1

Attention: Corporate Actions

Inquiries:

Toll-Free: 1-800-564-6253 (North America)

Phone: 1-514-982-7555 (Overseas)

E-Mail: corporateactions@computershare.com

Any questions and requests for assistance may be directed by

shareholders to Computershare Investor Services Inc. at the telephone numbers

and locations set out above.