<PAGE>   1
                                  UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549


                                    FORM 10-Q

(mark one)
  X     Quarterly report pursuant to Section 13 or 15(d) of the Securities
        Exchange Act of 1934 for the quarterly period ended September 30, 1997
        or
 
 ___    Transition report pursuant to Section 13 or 15(d) of the Securities
        Exchange Act of 1934

COMMISSION FILE NUMBER:  0-19454


                                  ANERGEN, INC.
             (Exact name of registrant as specified in its charter)



             CALIFORNIA                                          77-0183594
   (State or other jurisdiction of                            (I.R.S. Employer
   incorporation or organization)                            Identification No.)

         301 PENOBSCOT DRIVE
      REDWOOD CITY, CALIFORNIA                                      94063
(Address of principal executive offices)                         (Zip Code)

                        Telephone number: (650) 361-8901



Indicate by check mark whether the 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 preceding 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 [X]   No
                                       

At September 30, 1997, Registrant had outstanding 18,819,773 shares of Common
Stock.


<PAGE>   2
                                  ANERGEN, INC.

                                      INDEX
<TABLE>
<CAPTION>
PART I - FINANCIAL INFORMATION                                                       Page No.
                                                                                     --------
<S>             <C>                                                                    <C>
ITEM 1.        Financial Statements

               Condensed balance sheets - September 30, 1997
                 and December 31, 1996 .........................................         3

               Condensed statements of operations - three  and nine months
                 ended September 30, 1997 and 1996 .............................         4

               Condensed statements of cash flows - nine months
                 ended September 30, 1997 and 1996 .............................         5

               Notes to condensed financial statements .........................         6

ITEM 2.        Management's Discussion and Analysis of
                 Financial Condition and Results of Operations .................         7


PART II - OTHER INFORMATION

ITEM 6.        Exhibits and Reports on Form 8-K ................................        17

               Signatures ......................................................        18

</TABLE>
                                       2
<PAGE>   3
Part I:  Financial Information


                                  ANERGEN, INC.
                            CONDENSED BALANCE SHEETS
                      (IN THOUSANDS EXCEPT FOR SHARE DATA)
<TABLE>
<CAPTION>
                                   ASSETS
                                                            SEPTEMBER 30, 1997  DECEMBER 31, 1996
                                                            ------------------  -----------------
                                                                (UNAUDITED)
<S>                                                            <C>               <C>        
Current assets:
    Cash and cash equivalents ............................     $   5,309         $     3,963
    Short-term investments ...............................         4,219              12,437
    Contract receivables - including related party .......         1,209                 320
    Prepaid expenses......................................            90                 208
                                                               ---------           ---------
               Total current assets ......................        10,827              16,928
Property and equipment, net...............................         1,847               1,459
Other assets..............................................            36                  36
                                                               ---------           ---------

                                                               $  12,710           $  18,423
                                                               =========           =========
                    LIABILITIES AND SHAREHOLDERS' EQUITY
Current liabilities:
    Accounts payable  and accrued liabilities.............     $   1,308          $    1,326
    Current portion of capital lease obligations and debt.           471                 728
                                                               ---------           ---------

               Total current liabilities..................         1,779               2,054
Long-term portion of capital lease obligations and debt...           830                 366
Commitments
Shareholders' equity:
    Preferred stock, no par value;  none issued and
outstanding    ...........................................             -                   -
    Common stock, no par value;  40,000,000 shares
         authorized;  18,819,773 issued and outstanding
         (18,780,697 at December 31, 1996) ...............        57,586              57,484
    Additional paid-in-capital............................           659                 659
    Unrealized gain (loss) on investments.................             3                (34)
    Accumulated deficit...................................      (48,147)            (42,106)
                                                               ---------           ---------
               Total shareholders' equity.................        10,101              16,003
                                                               ---------           ---------
                                                               $  12,710           $  18,423
                                                               =========           =========
</TABLE>

Note:   The balance sheet at September 30, 1997 is derived from unaudited
        financial statements. The December 31, 1996 information is derived from
        audited financial statements at that date, but does not include all of
        the information and footnotes required by generally accepted accounting
        principles for complete financial statements.
                             See accompanying notes.



                                       3
<PAGE>   4

                                  ANERGEN, INC.
                       CONDENSED STATEMENTS OF OPERATIONS
                     (IN THOUSANDS EXCEPT PER SHARE AMOUNTS)
                                   (UNAUDITED)
<TABLE>
<CAPTION>
                                                 THREE MONTHS  ENDED      NINE MONTHS ENDED
                                                   SEPTEMBER 30,              SEPTEMBER 30,
                                                ---------------------     -------------------
                                                   1997       1996          1997        1996
                                                ---------- ----------     ---------  --------
<S>                                               <C>           <C>        <C>          <C>   
Revenues:
    Contract revenues, including related
      parties                                     $1,302        $864       $4,464       $2,286
    License fee                                       --       2,000           --        2,000
    Interest income                                  161         167          460          426
                                                --------      ------      -------      -------
                                                   1,463       3,031        4,924        4,712

Expenses:
    Research and development                       2,902       2,389        8,611        6,229
    General and administrative                       587         716        2,180        1,775
    Interest expense                                  70          38          174          137
                                                --------      ------      -------      -------
                                                   3,559       3,143       10,965        8,141
                                                --------      ------      -------      -------
Net loss                                        $ (2,096)     $ (112)     $(6,041)     $(3,429)
                                                ========      ======       ======      =======
Net loss per share                              $  (0.11)     $(0.01)      $(0.32)     $ (0.22)
                                                ========      ======       ======      =======

Shares used in calculating per share data         18,820      17,077       18,807       15,714
                                                ========      ======       ======       =======
</TABLE>



                             See accompanying notes.


                                       4
<PAGE>   5
                                  ANERGEN, INC.
                       CONDENSED STATEMENTS OF CASH FLOWS
                                 (IN THOUSANDS)
                                   (UNAUDITED)
<TABLE>
<CAPTION>
                                                            NINE MONTHS ENDED
                                                               SEPTEMBER 30,
                                                           1997            1996
                                                          --------     --------
<S>                                                        <C>          <C>     
Cash flows provided by (used in) operating activities:
  Net loss                                                 $(6,041)     $(3,429)
  Adjustments to reconcile net loss to net cash
  used in operating activities:
    Depreciation and amortization                              633          824
  Changes in operating assets and liabilities:
    Contract receivables - related party                      (889)        (178)
    Prepaid expenses                                           118          (43)
    Accounts payable and accrued liabilities                   (18)          68
                                                          --------     --------
Net cash used in operating activities                       (6,197)      (2,758)

Cash flows provided by (used in) investing activities:
  Purchase of investments available-for-sale               (20,946)     (21,985)
  Sale of investments available-for-sale                    29,201       15,565
  Purchase of property and equipment                        (1,021)        (451)
                                                          --------     --------
Net cash provided by (used in) investing
activities                                                   7,234       (6,871)
                                                          --------     --------

Cash flows provided by (used in) financing activities:
  Proceeds from facility and equipment debt
  financing                                                    659           --
  Repayments of capital lease obligations and debt            (452)        (704)
  Issuance of common stock, net                                102       10,003
                                                          --------     --------
Net cash provided by (used in) financing activities            309        9,299

Net increase (decrease) in cash                              1,346         (330)
Cash  and cash equivalents at beginning of period            3,963          468
                                                          --------     --------
Cash  and cash equivalents at end of period                  5,309          138
Short-term investments at end of period                      4,219       17,387
                                                          --------     --------
Cash, cash equivalents and short-term
investments at end of period                                $9,528      $17,525
                                                          ========     ========

</TABLE>


                             See accompanying notes.


                                       5
<PAGE>   6

                                  ANERGEN, INC.
                     NOTES TO CONDENSED FINANCIAL STATEMENTS
                               SEPTEMBER 30, 1997
                                   (UNAUDITED)


1. NATURE OF BUSINESS

        Anergen, Inc. (the "Company") was incorporated on April 26, 1988 for
        the purpose of developing therapies using biopharmaceutical compounds
        for the treatment of autoimmune diseases.

2. BASIS OF PRESENTATION

        The interim financial statements included herein have been prepared by
        the Company and have not been audited, pursuant to the rules and
        regulations promulgated by the Securities and Exchange Commission (the
        "Commission"). Certain information and footnote disclosures, normally
        included in financial statements prepared in accordance with generally
        accepted accounting principles, have been omitted pursuant to Commission
        rules and regulations; nevertheless, the Company believes that the
        disclosures are adequate to make the information presented not
        misleading. These condensed financial statements should be read in
        conjunction with the audited financial statements and notes thereto
        contained in the Company's Annual Report on Form 10-K for the year ended
        December 31, 1996. In the opinion of management, all adjustments,
        consisting only of normal recurring adjustments, necessary to present
        fairly the financial position of the Company (subject to year-end
        adjustments) with respect to the interim financial statements, and of
        the results of its operations and cash flows for the interim periods
        then ended, have been included. The results of operations for the
        interim periods are not necessarily indicative of the results for the
        full year.

        Net Loss Per Share

        Net loss per share is computed using the weighted average number of
        shares of common stock outstanding. In February 1997, the Financial
        Accounting Standards Board issued Statement 128, Earnings per Share,
        which is required to be adopted on December 31, 1997. At that time, the
        Company will be required to change the method currently used to compute
        loss per share and to restate all prior periods. Under the new
        requirements for calculating primary earnings per share, the dilutive
        effect of stock options will be excluded. The Company currently excludes
        common equivalent shares from outstanding stock options and warrants
        from the computation as their effect is anti-dilutive. The Company does
        not expect there to be a material impact on the net loss per share
        calculation upon adoption of Statement 128.



                                       6
<PAGE>   7

ITEM 2.                MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL
                             CONDITION AND RESULTS OF OPERATIONS

        Management's Discussion and Analysis of Financial Condition and Results
of Operations contains certain forward-looking statements which involve risks
and uncertainties. The Company's actual results could differ materially from the
results anticipated in these forward-looking statements as a result of certain
factors set forth hereunder and in the Company's Annual Report as filed on Form
10-K filed with the Securities and Exchange Commission for the year ended
December 31, 1996.

LIQUIDITY AND CAPITAL RESOURCES

        To date, the Company has financed its operations primarily through
        private placements of its equity securities with venture capitalists
        (which raised an aggregate of approximately $7.6 million in net
        proceeds), through the sale of its Common Stock to Novo Nordisk A/S
        (which raised approximately $8 million in net proceeds), through the
        issuance of its Common Stock and Warrants to purchase shares of Common
        Stock through a private placement in exchange for $1.5 million in
        proceeds, and through public offerings of its Common Stock which have
        raised an aggregate of $38.8 million in net proceeds, including $9.4
        million in net proceeds from the sale of 3.5 million shares of Common
        Stock to the public in August 1996 and approximately $500,000 from the
        underwritersi exercise of the over-allotment option in September 1996.
        The Company's cash, cash equivalents and short-term investments at
        September 30, 1997 were approximately $9.5 million, a decrease from
        $16.4 million due to cash used in operations and timing of receipts of
        contract receivables. Accounts payable and accrued liabilities decreased
        to $1,308,000 at September 30, 1997 from $1,326,000 at December 31,
        1996. Long-term debt increased from $366,000 at December 31, 1996 to
        $830,000 at September 30, 1997 due to the debt financing of equipment
        purchases. The Company had shareholders' equity at June 30, 1997 of
        approximately $10.1 million.

        The Company anticipates that its current cash, cash equivalents,
        short-term investments and expected revenues under its collaborative
        agreements will be sufficient to fund its operations through
        approximately 1998. Thereafter, the Company will require substantial
        additional funds to continue its operations. The Company anticipates
        that its current resources will be primarily used to fund clinical
        testing of AnervaX(TM) for Rheumatoid Arthritis ("RA"), manufacturing of
        GMP grade material for the Phase I clinical trial of the Company's
        AnergiX(TM) for Multiple Sclerosis ("MS") and the conduct of such trial
        and continued research and development and preparation for clinical
        testing of AnergiX for the treatment of RA, Type I Diabetes and
        Myasthenia Gravis ("MG"). The balance of such resources will be used to
        fund research on other autoimmune diseases ("IDDM") and general and
        administrative activities, including those associated with seeking
        collaborative arrangements to enable the Company to increase its
        research and development activities in other autoimmune diseases. 

        These foregoing forward-looking statements involve risks and
        uncertainties that could cause actual results to differ materially. In
        particular, the Company's capital requirements will vary depending on
        numerous factors many of which are outside the Company's control. These
        factors include the progress of the Company's research and development
        programs, manufacturing activities, the progress of the Company's
        clinical programs, the results of laboratory testing, the time and cost
        required to seek regulatory approvals to commence clinical trials for
        the Company's initial products, the need to obtain licenses to other
        proprietary rights, any required adjustments to the Company's operating
        plan to respond to competitive pressures or technological advances,
        developments with respect to the Company's existing or future
        collaborative arrangements, and the availability of various methods of
        financing. The Company expects to seek to raise additional capital
        through equity or debt financing, research and development
        collaborations with other pharmaceutical companies or through other
        sources. Any additional equity financing may be dilutive to
        shareholders, and debt financing, if available, may involve restrictions
        on stock dividends and other restrictions on the Company. Adequate funds
        for the Company's operations, whether from equity or debt, collaborative
        or other arrangements with corporate partners or from other sources, may
        not be available when needed or on terms attractive to the Company.
        Insufficient funds may require the Company to delay, scale back or
        eliminate some or all of its research and product development programs
        or to license third parties to commercialize products or technologies
        that the Company would otherwise seek to develop itself. The Company's
        liquidity will be reduced as amounts are expended for continuing
        research and development.


                                       7
<PAGE>   8

RESULTS OF OPERATIONS

        The Company's net loss increased by 1,771% to $2,096,000 in the fiscal
        quarter ended September 30, 1997 compared to a $112,000 loss in the
        corresponding period in the previous year. The increase was due to the
        lack of license fee revenue recognized in 1997 compared to a $2.0
        million license fee received in the previous year. Expenses increased
        13% to $3,559,000 in the fiscal quarter ended September 30, 1997
        compared to $3,143,000 in the corresponding period in the previous year,
        along with a net increase in contract revenues of 51% to $1,302,000 in
        the fiscal quarter ended September 30, 1997 compared to $864,000 in the
        corresponding period in the previous year. Total expenses increased
        primarily due to increased expenses for research and development related
        to clinical trials and development activities associated with the
        Company's collaborative arrangement with N. V. Organon. Research and
        development expenses increased 21% to $2,902,000 for the quarter ended
        September 30, 1997 from $2,389,000 in the corresponding period in the
        previous year due to an increase in clinical activities related to the
        Company's ongoing Phase IIa clinical trial of AnervaX for RA and an
        increase in manufacturing activities related to the Company's
        development of AnergiX for RA. The Company expects total operating
        expenses over time to increase as it increases research and development
        efforts.

        General and administrative expenses decreased 18% to $587,000 for the
        quarter ended September 30, 1997 compared to $716,000 in the
        corresponding period in the previous year primarily due to fewer costs
        associated with management transition and recruitment efforts.

        The increase in revenues was primarily due to revenues recorded in the
        current fiscal quarter related to the Company's collaborative agreement
        with N. V. Organon. Interest income decreased slightly to $161,000 for
        the quarter ended September 30, 1997 as compared to $167,000 in the
        corresponding period in the previous year. Interest income is expected
        to decline gradually over future periods as invested capital is used for
        operating activities. Interest expense increased to $70,000 for the
        quarter ended September 30, 1997 as compared to $38,000 in the
        corresponding period in the previous year due to higher debt balances as
        the Company financed capital purchases in 1997.

        The Company expects to incur substantial and increasing operating losses
        for at least the next several years. The Company's losses on a
        quarter-by-quarter basis may vary depending upon a variety of factors,
        any of which may fluctuate, including the level of research activities,
        the timing of hiring of additional scientific and management personnel,
        the retention of consultants, the purchase or leasing of laboratory
        equipment, the licensing of any required technology and other factors.
        Accordingly, the Company believes that quarter-by-quarter losses is not
        a useful indicator of the performance of the Company.

RISK FACTORS THAT MAY AFFECT FUTURE OPERATING PERFORMANCE

EARLY STAGE OF PRODUCT DEVELOPMENT; LACK OF COMMERCIAL PRODUCTS; NO ASSURANCE OF
SUCCESSFUL PRODUCT DEVELOPMENT

        The Company was founded in 1988 to discover and develop
        biopharmaceutical compounds for the treatment of autoimmune diseases. To
        achieve profitable operations, the Company, alone or with others, must
        successfully develop, obtain regulatory approval for, manufacture and
        market products. The Company does not have any products available for
        sale nor does it expect to have any products commercially available for
        at least several years, if at all. The Company's potential products are
        at the early stages of research and development, with only limited human
        testing of certain of the Company's products undertaken to date. The
        products currently under development by the Company will require
        significant additional research, laboratory testing and clinical trials
        and investment of capital prior to their commercialization. There can be
        no assurance that any potential products will be successfully developed,
        prove to be safe and efficacious in clinical trials, meet applicable
        regulatory standards, be capable of being produced in commercial
        quantities at acceptable costs or be successfully marketed.


                                       8
<PAGE>   9
LIMITED OPERATING HISTORY; HISTORY OF LOSSES

        The Company has experienced significant net losses every year since its
        inception in 1988. Net losses for the quarters ended September 30, 1997
        and 1996 were approximately $2.1 million and $0.1 million, respectively,
        and the Company had an accumulated deficit of approximately $48.1
        million as of September 30, 1997. The Company expects to incur
        substantial and increasing operating losses for at least the next
        several years. The amount of net losses and the time required by the
        Company to reach profitability are highly uncertain. There can be no
        assurance that the Company will ever be able to generate product revenue
        or achieve profitability on a substantial basis or at all. See
        "Management's Discussion and Analysis of Financial Condition and Results
        of Operations."

FUTURE REQUIREMENT FOR SIGNIFICANT ADDITIONAL CAPITAL

        The Company anticipates that its current cash, cash equivalents,
        short-term investments and expected revenues under its collaborative
        agreements will be sufficient to fund its operations through
        approximately 1998. Thereafter, the Company will require substantial
        additional funds to continue its operations. The Company anticipates
        that its current resources will be primarily used to fund clinical
        testing of AnervaX for RA and AnergiX for MS, and continued research and
        development and preparation for clinical testing of AnergiX for the
        treatment of RA, IDDM and MG. The balance of such resources will be used
        to fund research on other autoimmune diseases and general and
        administrative activities, including those associated with seeking
        collaborative arrangements to enable the Company to increase its
        research and development activities in current and or other autoimmune
        diseases. The Company's working capital requirements over the next few
        years may vary depending upon numerous factors, including the progress
        of the Company's research and development programs, manufacturing
        activities, the progress of the Company's clinical programs, the results
        of laboratory testing, the time and cost required to seek regulatory
        approvals to commence clinical trials for the Company's initial
        products, the need to obtain licenses to other proprietary rights, any
        required adjustments to the Company's operating plan to respond to
        competitive pressures or technological advances, developments with
        respect to existing or future collaborative arrangements and the
        availability of various methods of financing. The Company expects to
        seek to raise additional capital through equity or debt financing,
        research and development collaborations with corporate partners or
        through other sources. Any additional equity financing may be dilutive
        to shareholders, and debt financing, if available, may involve
        restrictions on stock dividends and other restrictions on the Company.
        Adequate funds for the Company's operations, whether from equity or debt
        financings, collaborative or other arrangements with corporate partners
        or from other sources, may not be available when needed or on terms
        attractive to the Company. Insufficient funds may require the Company to
        delay, scale back or eliminate some or all of its research and product
        development programs or to license third parties to commercialize
        products or technologies that the Company would otherwise seek to
        develop itself. The Company's liquidity will be reduced as amounts are
        expended for continuing research and development. See "Management's
        Discussion and Analysis of Financial Condition and Results of
        Operations-Liquidity and Capital Resources."

UNCERTAINTIES RELATED TO PRECLINICAL AND CLINICAL TRIALS

        Before obtaining regulatory approvals for the commercial sale of any of
        its products under development, the Company must demonstrate through
        preclinical studies and clinical trials that the product is safe and
        efficacious for use in each target indication. The results from
        preclinical studies and early clinical trials may not be predictive of
        results that will be obtained in large-scale testing, and there can be
        no assurance that the Company's clinical trials will demonstrate the
        safety and efficacy of any products or will result in any marketable
        products. A number of companies in the biotechnology industry have
        suffered significant setbacks in advanced clinical trials, even after
        promising results in earlier trials. The failure to adequately
        demonstrate the safety and efficacy of a therapeutic product under
        development could delay or prevent regulatory approval of the product
        and could have a material adverse effect on the Company.

        The rate of completion of the Company's clinical trials is dependent
        upon, among other factors, the FDA's willingness to allow Anergen to
        proceed; the results of Anergen's continued research and development,
        including test results and success in producing the epitopes and HLA
        molecules for each AnergiX compound; the number of skilled scientists,
        clinicians, and consultants the Company is able to employ in its efforts
        and the general interest in the medical community in a therapeutic using
        the Company's approach for treatment of the diseases targeted by the
        Company. Currently, the Company does not anticipate establishing its own
        clinical trials facility. The rate of completion of clinical trials is
        also dependent on patient enrollment, which is a function of many
        factors, including the size of the patient population, the proximity of
        patients to clinical sites and the existence of competitive trials. If
        the Company is unable to successfully complete its clinical trials, its
        business, financial condition and results of operations could be
        materially and adversely affected.

                                       9
<PAGE>   10
UNCERTAINTY OF MARKET ACCEPTANCE

        Even if the requisite regulatory approvals are obtained for the
        Company's potential products or for products developed in collaboration
        with the Company, uncertainty exists as to whether such products will be
        accepted by the market. A number of factors also may limit the market
        acceptance of a product which may be developed by, or discovered through
        collaboration with, the Company, including the rate of adoption by
        health care practitioners, the indications for which the product is
        approved, the rate of the product's acceptance by the target population,
        the timing of market entry relative to competitive products, the
        availability of alternative therapies, the price of the Company's
        product relative to alternative therapies, the availability of
        third-party reimbursement and the extent of marketing efforts by the
        Company and third-party distributors or agents retained by the Company.
        Side effects or unfavorable publicity concerning a Company product or
        any similar product could have an adverse effect on the Company's
        ability to obtain physician, patient or third-party payor acceptance and
        on efforts to sell that product. There can be no assurance of the
        Company's ability, or the length of time required, to achieve
        commercialization of the Company's products or that physicians, patients
        or third party payors will accept any of the Company's products as
        readily as alternative therapies, or at all.

GOVERNMENT REGULATION; NO ASSURANCE OF OBTAINING PRODUCT APPROVALS

        The Company's research and development activities are subject to
        regulation by numerous governmental authorities in the United States and
        other countries. Further, the future production and marketing of any
        products developed by the Company would also be regulated, particularly
        as to safety and efficacy. In the United States, vaccines, drugs and
        biologics are subject to rigorous FDA review. The Federal Food, Drug,
        and Cosmetic Act, the Public Health Service Act and other federal
        statutes and regulations govern or influence the testing, manufacture,
        safety, labeling, storage, record keeping, approval, advertising and
        promotion of such products. Noncompliance with applicable requirements
        can result in fines, recall or seizure of products, clinical study
        holds, total or partial suspension of production, refusal of the
        government to approve NDAs, PLAs, ELAs or allow the Company to enter
        into supply contracts and criminal prosecution. The FDA also has the
        authority to revoke PLAs and ELAs previously granted.

        In order to obtain FDA approval of a new biological product, the Company
        must submit proof of safety, purity, potency and efficacy. In most cases
        such proof entails extensive pre-clinical, laboratory, and clinical
        tests. The testing, preparation of necessary marketing applications and
        processing of those applications by the FDA is expensive and time
        consuming, can vary based on the type of product, and may take several
        years to complete. There is no assurance that the FDA will act favorably
        or quickly in making such reviews, and significant difficulties or costs
        may be encountered by the Company in its efforts to obtain FDA approvals
        that could delay or preclude the Company from marketing any products it
        may develop or furnish an advantage to competitors. The FDA may also
        require post-marketing testing and surveillance to monitor the effects
        of approved products or place conditions on any approvals that could
        restrict the commercial applications of such products. Product approvals
        may be withdrawn if compliance with regulatory standards is not
        maintained or if problems occur following initial marketing. In
        addition, delays imposed by the governmental approval process may
        materially reduce the period during which the Company may have the
        exclusive right to exploit patented products or technologies.

        The FDA approval process for a new biological drug involves completion
        of pre-clinical studies which include laboratory tests and animal
        studies to assess safety and effectiveness of the drug. Among other
        things, the results of these studies as well as how the product will be
        manufactured, are submitted to the FDA in an IND and, unless the FDA
        objects, the IND becomes effective 30 days following receipt by the FDA.
        FDA cleared human clinical trials may then be conducted. The results of
        the clinical trials are submitted to the FDA as part of a PLA. In
        addition to obtaining FDA approval for each AnergiX indication, an ELA
        must be filed and the FDA must approve the manufacturing facilities for
        the product. Product sales may commence only if the PLA and ELA are
        approved. Regulatory requirements for obtaining such FDA approvals are
        rigorous and there can be no assurance that such approvals will be
        obtained on a timely basis or at all.

                                       10
<PAGE>   11

        Sales of pharmaceutical products outside the United States are subject
        to foreign regulatory requirements that vary widely from country to
        country. The time required to obtain approvals required by foreign
        countries may be longer or shorter than that required for FDA approval,
        and requirements for licensing may differ from FDA requirements.

        If approval is obtained, the Company will be subject to continuing FDA
        obligations. When manufacturing biologics, the Company will be required
        to adhere to regulations setting forth current Good Manufacturing
        Practices ("GMP"), which require that the Company manufacture its
        products and maintain its records in a prescribed manner with respect to
        manufacturing, testing and quality control activities. Further, the
        Company must pass a preapproval inspection of its manufacturing
        facilities by the FDA before obtaining approval.

        Satisfaction of these FDA requirements, or similar requirements by
        foreign regulatory agencies, typically takes several years and the time
        needed to satisfy them may vary substantially, based upon the type,
        complexity and novelty of the pharmaceutical product. The effect of
        government regulation may be to delay or to prevent marketing of
        potential products for a considerable period of time and to impose
        costly procedures upon the Company's activities. There can be no
        assurance that the FDA or any other regulatory agency will grant
        approval for any products or indications being developed by the Company
        on a timely basis, or at all. Success in preclinical or early stage
        clinical trials does not assure success in later stage clinical trials.
        Data obtained from preclinical and clinical activities are susceptible
        to varying interpretations which could delay, limit or prevent
        regulatory approval. If regulatory approval of a product is granted,
        such approval may impose limitations on the indicated uses for which a
        product may be marketed. Further, even if regulatory approval is
        obtained, later discovery of previously unknown problems with a product
        may result in restrictions on the product, including withdrawal of the
        product from the market. Delay in obtaining or failure to obtain
        regulatory approvals would have a material adverse effect on the
        Company's business, financial condition and results of operations.

DEPENDENCE UPON COLLABORATIVE PARTNERS

        The Company's strategy for the development, clinical trials,
        manufacturing and commercialization of its products includes maintaining
        and entering into various collaborations with corporate partners,
        licensors, licensees and others. To date, the Company has entered into
        collaborative arrangements with Novo Nordisk with respect to the
        Company's AnergiX compounds for the treatment of MS, MG and IDDM, and
        with Organon with respect to an AnergiX compound for the treatment of
        RA. There can be no assurance that the interests and motivations of the
        Company's collaborators are, or will remain, aligned with those of the
        Company or that such collaborators will successfully perform their
        development, regulatory compliance, manufacturing or marketing functions
        or that such collaborations in whole or in part will continue. There can
        also be no assurance that the Company will be able to negotiate
        additional collaborative arrangements in the future on acceptable terms,
        if at all, or that any such collaborative arrangements will be
        successful. To the extent that the Company is not able to maintain or
        establish such arrangements, the Company would be required to undertake
        such activities at its own expense, which would significantly increase
        the Company's capital requirements and limit the programs the Company is
        able to pursue. In addition, the Company may encounter significant
        delays in introducing its products into certain markets or find that the
        development, manufacture or sale of its products in such markets is
        adversely affected by the absence of such collaborative agreements.

        The Company's current collaborative agreement with Novo Nordisk (Novo),
        which is focused on AnergiX MS, expires on August 31, 1998. The Company
        expects that Novo will fully fund the program until the conclusion of
        the current agreement. Novo has publicly disclosed a de-emphasis on
        research and development on drugs for central nervous system diseases.
        Novo and the Company have begun discussions on the future of the
        collaboration between the two companies. In the event of a decision by
        Novo to end the relationship, the Company's current intention would be
        to continue development of the AnergiX MS program with a new partner.

        The Company cannot control the amount and timing of resources which its
        collaborative partners devote to the Company's program or potential
        products, which can vary because of factors unrelated to the potential
        product. Collaborator participation will depend not only on the
        achievement of research and development objectives by the Company and
        its collaborators, which cannot be assured, but also on each
        collaborator's own financial, competitive, marketing and strategic
        considerations, which are outside the Company's control. Such strategic
        considerations may include the relative advantages of alternative
        products being marketed or developed by others, including relevant
        patent and proprietary positions. The Company's collaborative partners
        may develop, either alone or with others, products that compete with the
        development and marketing of the Company's


                                       11
<PAGE>   12
        products. Competing products, either developed by the collaborative
        partners or to which the collaborative partners have rights, may result
        in their withdrawal of support with respect to all or a portion of the
        Company's technology, which would have a material adverse effect on the
        Company's business, financial condition and results of operations. If
        Novo Nordisk, Organon or any future collaborative partner breaches or
        terminates their agreements with the Company or otherwise fails to
        conduct their collaborative activities in a timely manner, the
        preclinical or clinical development or commercialization of product
        candidates or research programs will be delayed, and the Company will be
        required to devote additional resources to product development and
        commercialization or terminate or severely limit certain development
        programs. There also can be no assurance that disputes will not arise in
        the future with respect to the ownership of rights to any technology
        developed with third parties. These and other possible disagreements
        between collaborators and the Company could lead to delays in the
        collaborative research, development and commercialization of certain
        product candidates or could require or result in litigation or
        arbitration, which would be time consuming and expensive, and would have
        a material adverse effect on the Company's business, financial condition
        and results of operations. See "Management's Discussion and Analysis of
        Financial Condition and Results of OperationsoLiquidity and Capital
        Resources".

UNCERTAINTY RELATING TO PATENTS AND PROPRIETARY RIGHTS

        The Company's success will depend in significant part on its ability to
        maintain patent protection for its therapeutic approach and for any
        developed products, to preserve its trade secrets and to operate without
        infringing the proprietary rights of third parties. Although the Company
        has obtained patents covering certain aspects of its technology, no
        assurance can be given that additional patents will be issued or, if
        issued, that the scope of any patent protection will be significant, or
        that the patents will be held valid if subsequently challenged.
        Moreover, the Company cannot ascertain with certainty that no patent
        conflict will exist with other products or processes which could compete
        with the Company's approaches.

        Because of the length of time and expense associated with bringing new
        products through development and to the marketplace, and the length of
        time required for the governmental approval process, the pharmaceutical
        industry has traditionally placed considerable importance on obtaining
        and maintaining patent and trade secret protection for significant new
        technologies, products and processes. The Company and other
        biotechnology and pharmaceutical firms have applied, and are applying,
        for patents for their products and certain aspects of their
        technologies. The enforceability of patents issued to biotechnology and
        pharmaceutical firms is highly uncertain. Federal court decisions
        indicating legal considerations surrounding the validity of patents in
        the field are in transition, and there can be no assurance that the
        historical legal standards surrounding questions of validity will
        continue to be applied or that current defenses as to issued patents in
        the field will offer protection in the future. In addition, there can be
        no assurance as to the degree and range of protection any patents will
        afford, whether patents will issue or the extent to which the Company
        will be successful in not infringing patents granted to others.

        While the Company pursues patent protection for products and processes
        where appropriate, it also relies on trade secrets, know-how and
        continuing technological advancement to develop and maintain its
        competitive position. The Company's policy is to have each employee
        enter into an agreement that contains provisions prohibiting the
        disclosure of confidential information to anyone outside the Company.
        Research and development contracts and relationships between the Company
        and its scientific consultants provide access to aspects of the
        Company's know-how that is protected generally under confidentiality
        agreements with the parties involved. There can be no assurance,
        however, that these confidentiality agreements will be honored or that
        the Company can effectively protect its rights to its unpatented trade
        secrets. Moreover, there can be no assurance that others will not
        independently develop substantially equivalent proprietary information
        and techniques or otherwise gain access to the Company's trade secrets.

        The Company may be required to obtain licenses to patents or other
        proprietary rights from third parties. There can be no assurance that
        any licenses required under any patents or proprietary rights will be
        made available on terms acceptable to the Company, if at all. If the
        Company does not obtain required licenses, it could encounter delays in
        product development while it attempts to redesign products or methods or
        it could find that the development, manufacture or sale of products
        requiring such licenses could be foreclosed.

        The Company is aware of a European patent and corresponding U.S. and
        Australian patents which contain claims that relate to certain of the
        Company's proposed products and their uses. In accordance with European
        Patent


                                       12
<PAGE>   13

        Office ("EPO") procedures, third parties can oppose an EPO patent grant
        by presenting information which they believe justifies narrowing or
        revoking the grant of the patent. The Company is opposing the
        aforementioned grant in the EPO. There can, however, be no assurance
        that the granted EPO claims will be revoked or significantly narrowed in
        scope as a result of the opposition proceeding. If valid claims in these
        patents are found to be infringed by the Company's products, the
        Company's ability to make, use, offer to sell, or sell, such products
        could be materially and adversely affected. In addition, the Company
        could incur substantial costs in defending any patent litigation brought
        against it or in asserting the Company's patent rights, including those
        licensed to the Company by others, in a suit against another party. The
        United States Patent and Trademark Office (the "USPTO") could institute
        interference proceedings in connection with one or more of the Company's
        patents or patent applications which proceedings could result in an
        adverse decision as to priority of an invention. The USPTO also could
        institute reexamination proceedings in connection with one or more of
        the Company's patents or patent applications, which could result in an
        adverse decision as to the patents' validity or scope.

NEED TO DEVELOP MANUFACTURING CAPABILITIES

        The Company has no volume manufacturing capacity or experience in volume
        manufacturing of pharmaceutical or other biological products.
        Establishing its own volume manufacturing capabilities would require
        significant scale-up expenses and additions to facilities and personnel.
        In addition, the Company must successfully develop the process required
        for volume manufacturing. The pharmaceutical products under development
        by the Company have never been manufactured on a commercial scale and
        there can be no assurance that such products can be manufactured at a
        cost or in quantities to make them commercially viable. The Company will
        be required to establish arrangements with contract manufacturers to
        supply a portion of its compounds for subsequent clinical trials as well
        as the manufacture, packaging, labeling and distribution of finished
        products. If the Company is unable to contract for sufficient supply of
        a portion of its compounds on acceptable terms, and it is unable to
        develop the capability to produce the epitopes internally, the Company's
        human clinical testing schedule would be delayed, resulting in the delay
        of submission of products for regulatory approval and initiation of new
        development programs, which would have a material adverse effect on the
        Company. If the Company should encounter delays or difficulties in
        establishing relationships with manufacturers to produce, package and
        distribute its finished products, market introduction and subsequent
        sales of such products would be adversely affected. Moreover, contract
        manufacturers that the Company may use must adhere to current GMP
        regulations enforced by the FDA through its facilities inspection
        program. If these facilities cannot pass a pre-approval plant
        inspection, the FDA pre-market approval of the products will be
        adversely affected.

LACK OF MARKETING EXPERIENCE; DEPENDENCE ON THIRD PARTIES

        The Company currently has no sales, marketing or distribution
        capability. The Company intends to rely on relationships with one or
        more pharmaceutical companies with established distribution systems and
        direct sales forces to market its products. In the event that the
        Company is unable to reach agreement with one or more pharmaceutical
        companies to market its products, it may be required to market its
        products directly and to develop a marketing and sales force with
        technical expertise and supporting distribution capability. There can be
        no assurance that the Company will be able to establish in-house sales
        and distribution capabilities or relationships with third parties, or
        that it will be successful in gaining market acceptance for its
        products. To the extent that the Company decides to utilize existing or
        future co-promotion or other licensing arrangements, the Company must
        develop its own sales, marketing or distribution capability, and there
        can be no assurance that such efforts will be successful.

COMPETITION AND TECHNOLOGICAL CHANGE

        The biotechnology and pharmaceutical industries are characterized by
        rapidly evolving technology and intense competition. The Company's
        competitors include major pharmaceutical, chemical and specialized
        biotechnology companies, most of which have financial, technical,
        research and development, manufacturing, clinical and marketing
        resources significantly greater than those of the Company. The Company
        believes that these other entities recognize the need for effective
        therapies for the autoimmune diseases targeted by the Company and are
        highly motivated to develop such therapies. In addition, many
        specialized biotechnology companies have formed collaborations with
        large, established companies to support research, development and
        commercialization of products that may be competitive with those of the
        Company. Academic institutions, governmental agencies and other public
        and private research organizations are also conducting research
        activities and seeking patent


                                       13
<PAGE>   14
        protection and may commercialize products on their own or through joint
        ventures. The Company is aware of certain products in development by
        competitors that are intended to be used for the prevention or treatment
        of certain diseases the Company has targeted for product development.

        The existence of these products, or other products or treatments of
        which the Company is not aware, or products or treatments that may be
        developed in the future which may be more effective, may adversely
        affect the commercialization or marketability of products which may be
        developed by the Company or potentially render the Company's technology
        obsolete or non-competitive.

        The Company's competitive position will depend on its ability to attract
        and retain qualified scientific and other personnel, develop effective
        proprietary products, implement production and marketing plans, obtain
        patent protection and secure adequate capital resources. In addition,
        the first pharmaceutical product to reach the market in a therapeutic or
        preventive area is often at a significant competitive advantage relative
        to later entrants to the market. The Company expects its products, if
        approved for sale, to compete primarily on the basis of product
        efficacy, safety, patent position, reliability, price and patient
        convenience.

UNCERTAINTY RELATED TO PHARMACEUTICAL PRICING AND REIMBURSEMENT

        Political, economic and regulatory influences are subjecting the health
        care industry in the United States to fundamental change. Initiatives to
        reduce the federal deficit and to reform health care delivery are
        increasing these cost containment efforts. The Company anticipates that
        Congress, state legislatures and the private sector will continue to
        review and assess alternative benefits, controls on health care spending
        through limitations on the growth of private health insurance premiums
        and Medicare and Medicaid spending, the creation of large insurance
        purchasing groups, price controls on pharmaceuticals and other
        fundamental changes to the health care delivery system. Any such
        proposed or actual changes could cause existing and potential partners
        of the Company to limit or eliminate spending on collaborative
        development projects. Legislative debate is expected to continue in the
        future, market forces are expected to demand reduced costs and Anergen
        cannot predict what impact the adoption of any federal or state health
        care reform measures or future private sector reforms may have on its
        business.

        In both domestic and foreign markets, sales of the Company's proposed
        products will depend in part upon the availability of reimbursement from
        third-party payors, such as government health administration
        authorities, private health insurers and other organizations. In
        addition, other third-party payors are increasingly challenging the
        price and cost effectiveness of medical products and services.
        Significant uncertainty exists as to the reimbursement status of newly
        approved health care products. There can be no assurance that the
        Company's potential products or products discovered in collaboration
        with the Company will be considered cost-effective or that adequate
        third-party reimbursement will be available to enable Anergen to
        maintain price levels sufficient to realize an appropriate return on its
        significant investment in product research and development. Legislation
        and regulations affecting the pricing of pharmaceuticals may change
        before the Company's proposed products are approved for marketing.
        Adoption of such legislation could further limit reimbursement for
        medical products. If adequate coverage and reimbursement levels are not
        provided by the government and third-party payors for the Company's
        products, the market acceptance of these products would be adversely
        affected, which would have a material adverse effect on the Company's
        business, financial condition and results of operations.

DEPENDENCE ON AND NEED FOR ADDITIONAL KEY PERSONNEL; RELIANCE ON ACADEMIC
COLLABORATORS

        The success of the Company and of its business strategy is dependent in
        large part on the ability of the Company to attract and retain key
        management and operating personnel. Such persons are in high demand and
        are often subject to competing offers. The Company will need to develop
        expertise and add skilled employees or retain consultants in such areas
        as research and development, clinical testing, government approvals,
        marketing and manufacturing in the future. There can be no assurance
        that the Company will be able to attract and retain the qualified
        personnel or develop the expertise needed for its business. The loss of
        the services of one or more of the Company's officers or other members
        of the research or management group or the inability to hire additional
        personnel and develop expertise as needed would have a material adverse
        effect on the Company.

        A significant portion of the Company's research and development and
        clinical trials is conducted under sponsored research programs with
        several universities. The Company depends on the availability of the
        principal investigator for each such program, and the Company cannot
        assure that these individuals or their research staffs 


                                       14
<PAGE>   15
        will be available to conduct research and development or clinical
        trials. The Company's academic collaborators are not employees of the
        Company. As a result, the Company has limited control over their
        activities and can expect that only limited amounts of their time will
        be dedicated to Company activities. In addition, the Company's academic
        collaborators are employed by major institutions which have
        collaborative relationships with other parties, some of which may be
        competitors of the Company. Accordingly, there can be no assurance that
        research and development, preclinical and clinical testing performed by
        these collaborators will be completed in a timely manner, if at all, and
        any inability to do so could have a material adverse effect on the
        Company.

POTENTIAL PRODUCT LIABILITY

        The testing, marketing and sale of human health care products entail an
        inherent risk of exposure to product liability claims in the event that
        the use of the Company's technology or prospective products is alleged
        to have resulted in adverse effects. While the Company has taken, and
        will continue to take, what it believes are appropriate precautions to
        minimize exposure to product liability, there can be no assurance that
        it will avoid significant liability. The Company possesses limited
        general liability and product liability insurance related to its
        clinical trials of AnervaX for RA and to its clinical trials of AnergiX
        for MS and certain other types of insurance customarily obtained by
        business organizations. There can be no assurance that the existing
        insurance coverage is adequate or that it will avoid liability. The
        Company intends to seek insurance against product liability risks
        associated with the testing, manufacturing or marketing of its products.
        However, there can be no assurance that it will be able to obtain such
        insurance in the future, or that if obtained, such insurance will be
        sufficient in amount. Consequently, a product liability claim or other
        claims with respect to uninsured liabilities or in excess of insured
        liabilities could have a material adverse effect on the business or
        financial condition of the Company.

HAZARDOUS MATERIALS; ENVIRONMENTAL MATTERS

        The Company is subject to regulation by the Occupational Safety and
        Health Administration ("OSHA") and the Environmental Protection Agency
        ("EPA") and to regulation under the Toxic Substances Control Act, the
        Resource Conservation and Recovery Act and other regulatory statutes,
        and may in the future be subject to other federal, state or local
        regulations. Although the Company believes that it has complied with
        these laws, regulations and policies in all material respects and has
        not been required to take any significant action to correct any material
        noncompliance, there can be no assurance that the Company will not be
        required to incur significant costs to comply with environmental and
        health and safety regulations in the future. The Company's research and
        development involves the controlled use of hazardous materials,
        including but not limited to certain hazardous chemicals and radioactive
        materials. Although the Company believes that its safety procedures for
        handling and disposing of such materials comply with the standards
        prescribed by state and federal regulations, the risk of accidental
        contamination or injury from these materials cannot be eliminated. In
        the event of such an accident, the Company could be held liable for any
        damages that result and any such liability could exceed the resources of
        the Company. In addition, regulations may be promulgated governing
        biotechnology that may affect the Company's research and development
        programs. The Company is unable to predict whether any agency will adopt
        any regulation which would have a material adverse effect on the
        Company's business, financial condition and results of operations.

VOLATILITY OF STOCK PRICE

        The market price of the Company's Common Stock, similar to the
        securities of other biotechnology companies, has been and is likely to
        continue to be highly volatile. Announcements regarding the results of
        regulatory approval filings, clinical trials or other testing,
        technological innovations or new commercial products by the Company or
        its competitors, patents and intellectual property rights by the Company
        or its competitors, developments as to current or future collaborations
        by the Company or its competitors, government regulations, the status of
        health care reform initiatives, fluctuations in operating results,
        changes in recommendations by financial analysts, and general market
        conditions for biotechnology stocks could have a significant impact on
        the future price of the Common Stock. Trading volume of the Company's
        Common Stock has been relatively limited and sales of substantial
        amounts of Common Stock could have an adverse effect on the price of the
        Common Stock.

CONTROL BY EXISTING STOCKHOLDERS

                                       15
<PAGE>   16
        The Company's officers, directors and principal shareholders, namely
        Warburg, Pincus Ventures, L.P. ("Warburg"), International Biotechnology
        Trust PLC ("IBT"), and Novo Nordisk, collectively beneficially own
        approximately 50% of the Company's outstanding Common Stock. Under a
        March+1995 common stock purchase agreement with Warburg and IBT
        ("Warburg/IBT Purchase Agreement"), the Company is currently obligated
        to include in the slate of nominees recommended by the Company's Board
        of Directors and management, at each election of directors, two
        candidates selected by Warburg, one candidate selected by IBT and one
        candidate mutually agreed to by IBT and Warburg. Additionally, while not
        obligated to do so, since 1993, the Company has included a
        representative of Novo Nordisk in its slate of nominees for the Board of
        Directors. The ownership of the Company's Common Stock, and the ability
        to designate candidates for the Company's recommended slate of nominees
        for the Board of Directors, of Warburg, IBT and Novo Nordisk will enable
        such shareholders to have significant influence over major corporate
        transactions as well as the election of directors of the Company and
        control over board decisions and could have the effect of delaying,
        deterring or preventing a change in control of the Company.

ANTI-TAKEOVER PROVISIONS; POSSIBLE ISSUANCE OF PREFERRED STOCK OR ACCELERATION
OF OPTION VESTING

        The Board of Directors has authority, without further action by
        shareholders, to issue up to 10,000,000 shares of Preferred Stock with
        rights, preferences and privileges designated by the Board of Directors.
        This Preferred Stock could be issued quickly with terms calculated to
        delay or prevent a change in control of the Company or to make removal
        of management more difficult. In certain circumstances, such issuance
        could have the effect of decreasing the market price of the Common Stock
        or of delaying, deterring or preventing a change in control of the
        Company. The Company has no present plan to issue any shares of
        Preferred Stock. Further, pursuant to the Company's option plans, in the
        event of certain mergers of the Company with other entities, transfers
        of voting control of the Company's capital stock or sale of all or
        substantially all of the Company's assets, the Company's Board of
        Directors has the right under certain circumstances to cause all
        outstanding options to become fully vested prior to the event causing
        such acceleration and all unexercised options will terminate upon
        completion of such event.



                                       16
<PAGE>   17
                                  ANERGEN, INC.


PART II - OTHER INFORMATION


Item 1.  Legal Proceedings

         None

Item 2.  Changes in Securities and Use of Proceeds

         None

Item 3.  Defaults Upon Senior Securities

         None

Item 4.  Submission of Matters to a Vote of Security Holders

         None

Item 5.  Other Information

         None

Item 6.  Exhibits and reports on Form 8-K

         a)    Exhibits

        Exhibit    Description

        3.1(1)     Restated and Amended Articles of Incorporation.
        3.2(1)     Bylaws, as amended.
        4.1(1)     Form of Common Stock Certificate.
        27.1       Financial Data Schedule

           (1)   Incorporated by reference to the exhibit filed with
                 Registrant's Registration Statement on Form S-1 (No. 33-42107),
                 as amended.

         b)    Reports on Form 8-K. No reports on Form 8-K were filed by the
               Company during the quarter ended September 30, 1997.

                                       17
<PAGE>   18
                                    SIGNATURE


        Pursuant to the requirements 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.


                                  ANERGEN, INC.


Date: November 11, 1997            By:  /s/ DAVID V. SMITH
                                          ------------------
                                          David V. Smith
                                          Vice President, Finance and Chief
                                          Financial Officer on behalf of the
                                          Company and as principal financial
                                          and chief accounting officer

                                       18
<PAGE>   19
                               INDEX TO EXHIBITS
<TABLE>
<CAPTION>

EXHIBIT                  
NUMBER                   DESCRIPTION
-------                  ------------
<S>                      <C>
27.1                     Financial Data Schedule

</TABLE>