<PAGE>   1
                       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, 1996
         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: (415) 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, 1996, Registrant had outstanding 18,734,754 shares of Common
Stock.
<PAGE>   2
                                  ANERGEN, INC.

                                      INDEX

<TABLE>
Part I:  Financial Information                                                 Page No.
-------  ---------------------                                                 --------
<S>               <C>                                                         
ITEM 1.           Condensed Consolidated Financial Statements (unaudited)

                  Condensed balance sheets - September 30, 1996
                    and December 31, 1995.......................................  3

                  Condensed statements of operations - three and nine months
                    ended September 30, 1996 and 1995...........................  4

                  Condensed statements of cash flows - nine months ended
                    September 30, 1996 and 1995.................................  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..............................  9

                  Signatures.................................................... 10
</TABLE>
<PAGE>   3
Part I:  Financial Information


                                  ANERGEN, INC.
                            CONDENSED BALANCE SHEETS
                                 (IN THOUSANDS )

<TABLE>
<CAPTION>
                                            ASSETS
                                                                            SEPTEMBER 30, 1996     DECEMBER 31, 1995
                                                                            ------------------     -----------------
                                                                                (UNAUDITED)
<S>                                                                              <C>                     <C>     
Current assets:
     Cash and equivalents ........................................               $    138                $    468
     Short-term investments ......................................                 17,387                  11,024
     Contract receivables - related party ........................                    993                     815
     Prepaid expenses ............................................                    145                     102
                                                                                 --------                --------
                  Total current assets ...........................                 18,663                  12,409
Property and equipment, net ......................................                  1,648                   2,010
Other assets .....................................................                     36                      36
                                                                                 --------                --------
                                                                                 $ 20,347                $ 14,455
                                                                                 ========                ========
                             LIABILITIES AND SHAREHOLDERS' EQUITY
Current liabilities:
     Accounts payable and accrued liabilities ....................               $  1,108                $  1,040
     Current portion of capital lease obligations and debt .......                    722                     883
                                                                                 --------                --------

                  Total current liabilities ......................                  1,830                   1,923
Long-term portion of capital lease obligations and debt ..........                    275                     818
Commitments
Shareholders' equity:
     Preferred stock, no par value;  none issued and outstanding .                     --                      --
     Common stock, no par value;  40,000,000 shares authorized;
           18,734,025 issued and outstanding (14,967,680 at
           December 31, 1995).O ..................................                 57,362                  47,359
     Additional paid-in-capital ..................................                    659                     648
     Unrealized gain (loss) on investments .......................                    (41)                     16
     Accumulated deficit .........................................                (39,738)                (36,309)
                                                                                 --------                --------
                  Total shareholders' equity .....................                 18,242                  11,714
                                                                                 --------                --------
                                                                                 $ 20,347                $ 14,455
                                                                                 ========                ========
</TABLE>



                             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,
                                                             -------------                        -------------
                                                        1996              1995               1996               1995
                                                        ----              ----               ----               ----
<S>                                                 <C>                <C>                <C>                <C>     
Revenues:
     Contract revenues - related party ...          $    864           $    627           $  2,286           $  2,189
     License fee .........................             2,000                 --              2,000                 --
     Interest income .....................               167                185                426                352
                                                    --------           --------           --------           --------
                                                       3,031                812              4,712              2,541

Expenses:
     Research and development ............             2,389              2,101              6,229              6,331
     General and administrative ..........               716                448              1,775              1,375
     Interest expense ....................                38                 92                137                244
                                                    --------           --------           --------           --------
                                                       3,143              2,641              8,141              7,950
                                                    --------           --------           --------           --------
Net loss .................................          $   (112)          $ (1,829)          $ (3,429)          $ (5,409)
                                                    --------           --------           --------           --------

Net loss per
share ....................................          $  (0.01)          $  (0.12)          $  (0.22)          $  (0.45)
                                                    --------           --------           --------           --------

Shares used in calculating per share  data            17,077             14,943             15,714             12,149
                                                    --------           --------           --------           --------
</TABLE>



                             See accompanying notes.

                                       4
<PAGE>   5
                                  ANERGEN, INC.
                       CONDENSED STATEMENTS OF CASH FLOWS
                                 (IN THOUSANDS)
                                   (UNAUDITED)

<TABLE>
<CAPTION>

                                                                         NINE MONTHS ENDED
                                                                           SEPTEMBER 30,
                                                                      1996               1995
                                                                      ----               ----
<S>                                                               <C>                <C>      
Cash flows used in operating activities:
   Net loss ............................................          $ (3,429)          $ (5,409)
   Adjustments to reconcile net loss to net cash used in
   operating activities:
     Depreciation and amortization .....................               813                793
     Deferred compensation amortization ................                11                 36
   Changes in operating assets and liabilities:
     Contract receivables - related party ..............              (178)               112
     Prepaid expenses ..................................               (43)                62
     Other assets ......................................                --                (16)
     Accounts payable and accrued liabilities ..........                68                 18
                                                                  --------           --------
Net cash used in operating activities ..................            (2,758)            (4,404)

Cash flows provided by (used in) investing activities:
   Purchase of investments available-for-sale ..........           (21,985)           (27,353)
   Sale of investments available-for-sale ..............            15,565             16,952
   Purchase of property and equipment ..................              (451)              (747)
                                                                  --------           --------
Net cash used in investing activities ..................            (6,871)           (11,148)
                                                                  --------           --------

Cash flows provided by (used in) financing activities:
   Proceeds from facility and equipment  debt financing                 --                497
   Repayments of capital lease obligations and debt ....              (704)              (745)
   Issuance of common stock, net .......................            10,003             14,734
                                                                  --------           --------
Net cash provided by financing activities ..............             9,299             14,486

Net decrease in cash ...................................              (330)            (1,066)
Cash  and equivalents at beginning of period ...........               468              1,248
                                                                  --------           --------
Cash  and equivalents at end of period .................               138                182
Short-term investments at end of period ................            17,387             12,999
                                                                  --------           --------
Cash and short-term investments at end of period .......          $ 17,525           $ 13,181
                                                                  --------           --------
</TABLE>



                             See accompanying notes.

                                       5
<PAGE>   6
                                  ANERGEN, INC.
                     NOTES TO CONDENSED FINANCIAL STATEMENTS
                               SEPTEMBER 30, 1996
                                   (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 without audit, 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, 1995. 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.

         Loss Per Share

         Net loss per share is computed using the weighted average number of
         shares of common stock outstanding. Common equivalent shares from
         outstanding stock options and warrants are excluded from the
         computation as their effect is anti-dilutive.

3.    SIGNIFICANT EVENTS

         On August 9, 1996 the Company completed a follow-on offering of
         3,500,000 shares of its Common Stock in exchange for gross proceeds of
         $10.5 million. On September 12, 1996 the underwriters of the follow-on
         offering exercised a portion of their over-allotment option totaling 
         168,000 shares of Common Stock, raising the total gross proceeds from
         the offering to approximately $11.0 million.

         On September 2, 1996 the Company received a $2 million license fee
         related to its collaborative agreement which it entered into on June
         28, 1996 with N.V. Organon, of Oss, The Netherlands. Under the
         collaboration, the parties intend to develop a product to treat
         rheumatoid arthritis by utilizing a peptide discovered by N.V. Organon
         using the Company's proprietary AnergiX technology.



                                       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, in the Company's Annual Report as filed on Form
10-K and Form 10-K/A filed with the Securities and Exchange Commission, and in
the Registration Statement as filed on Form S-1 by the Company in August 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 $9.5
         million in net proceeds from the sale of 3.5 million shares of Common
         Stock to the public in August 1996 (the "1996 Follow-on Offering") and
         an additional $469,000 from the underwriters' exercise of the
         over-allotment option in September 1996. The Company's cash, cash 
         equivalents and short-term investments at September 30, 1996 were
         approximately $17.5 million, representing an increase from the end of
         the previous quarter of approximately $9.8 million. The Company had
         shareholders' equity at September 30, 1996 of approximately $18.2
         million. Accounts payable and accrued liabilities increased to
         $1,108,000 at September 30, 1996 from $1,040,000 at December 31, 1995.
         Long-term debt decreased from $818,000 at December 31, 1995 to $275,000
         at September 30, 1996.

         The Company anticipates that its current cash, short-term investments
         and expected revenues under its collaborative agreements, combined with
         the net proceeds from the 1996 Follow-on Offering, will be sufficient
         to fund its operations for approximately two years. 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 the Company's ongoing Phase II clinical trials
         of AnervaX(TM) for rheumatoid arthritis, manufacturing of GMP grade
         material for the Phase I clinical trial of the Company's AnergiX(TM)
         for multiple sclerosis and the conduct of such clinical trial, research
         activities in its core AnervaX and AnergiX technologies to further
         current programs in rheumatoid arthritis, multiple sclerosis, insulin
         dependent diabetes mellitus and myasthenia gravis and to develop
         programs in other autoimmune diseases, and to support research
         activities in academic institutions. The balance of such resources will
         be used to fund continued limited 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 other autoimmune
         diseases. The foregoing forward-looking statements involve risks and
         uncertainties that could cause actual results to differ materially. In
         particular, the Company's working capital requirements may vary
         depending on numerous factors that are beyond 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 either from the public equity market, private
         placements, and/or R&D collaborations with other pharmaceutical
         companies. Any additional equity financing may be dilutive to
         shareholders, and debt financing, if available, may involve
         restrictions on stock dividends. Adequate funds for the Company's
         operations, whether from financial markets, 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 decreased by 94% to $112,000 in the fiscal
         quarter ended September 30, 1996 compared to a $1,829,000 loss in the
         corresponding period in the previous year due to an increase in
         revenues of 273% to $3,031,000 in the fiscal quarter ended September
         30, 1996 compared to $812,000 in the corresponding period in the
         previous year. This increase in revenues was primarily due to a $2
         million license fee received in the third quarter related to the
         Company's collaborative agreement with N.V. Organon. Total expenses
         increased by 19% from $2,641,000 to $3,143,000 due primarily to
         increased expenses related to clinical trial and corporate development
         activities. The Company expects total operating expenses to increase as
         it increases research and development efforts.

         Research and development expenses increased 14% to $2,389,000 for the
         quarter ended September 30, 1996 from $2,101,000 in the corresponding
         period in the previous year. This is due to an increase in clinical
         activities related to the Company's AnergiX for multiple sclerosis
         which is in Phase I testing, and to an increase in clinical costs
         associated with the Company's ongoing Phase II clinical trial of
         AnervaX for rheumatoid arthritis. The Phase II clinical trial of
         AnervaX was initiated in June of 1996.

         General and administrative expenses increased 60% to $716,000 for the
         quarter ended September 30, 1996 compared to $448,000 in the
         corresponding period in the previous year primarily due to compensation
         costs associated with the retirement of John Fara, Ph.D., the former
         President and CEO, the recruitment and compensation costs related to
         the hiring of Barry Sherman, M.D., as President and CEO, costs related
         to additional recruitment efforts and increased corporate development
         activities.

         Interest income decreased to $167,000 for the quarter ended September
         30, 1996 as compared to $185,000 in the corresponding period in the
         previous year due to lower average cash balances in 1996. Interest
         expense decreased to $38,000 for the quarter ended September 30, 1996
         as compared to $92,000 in the corresponding period in the previous year
         due to lower debt balances. Interest income is expected to increase as
         a result of the investment of the net proceeds from the 1996 Follow-on
         Offering, and to decline gradually over future periods as invested
         capital is used for operating activities.

         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 will
         not be a useful indicator of the performance of the Company.

FACTORS THAT MAY AFFECT FUTURE OPERATING PERFORMANCE

         The factors discussed in Item 1 and Item 7 of the Company's Annual
         Report on Form 10-K and Form 10-K/A for fiscal year 1995 and the
         section entitled "Risk Factors" in the Company's Registration Statement
         as filed on Form S-1 in August 1996 are hereby incorporated by
         reference. Readers are cautioned that such factors, among others, in
         some cases have affected, and in the future could cause the Company's
         actual results to differ materially from those expressed in any
         forward-looking statements made by, or on behalf of, the Company.
         Factors that could cause actual results to differ include but are not
         limited to (i) the Company's ability to successfully develop and market
         its products, (ii) the extent to which the Company's products, if any,
         prove to be safe and efficacious in clinical trials, meet applicable
         regulatory standards and are capable of being produced in commercial
         quantities at acceptable costs, (iii) uncertainties related to
         preclinical and clinical trials including the rate of completion of the
         Company's clinical trials, (iv) market acceptance of the Company's
         products, if any, (v) government regulation and future health care
         legislation, (vi) the Company's success in maintaining existing and
         developing collaborations with corporate partners, licensors,
         licensees, and others, (vii) the Company's 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, (viii) competition and
         technological change, (ix) general economic conditions, (x) the
         Company's ability to attract and retain key management and skilled
         employees and (xi) potential liability claims and other litigation.



                                       8
<PAGE>   9
                                  ANERGEN, INC.

PART II:   Other Information

Item 1.    Legal Proceedings

           None

Item 2.    Changes in Securities

           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
<TABLE>
<CAPTION>

         Exhibit     Description                                                   Page
         -------     -----------                                                   ----
<S>      <C>                                                                        <C>
         3.1         Restated and Amended Articles of Incorporation.                (1)
         3.2         Bylaws, as amended.                                            (1)
         4.1         Form of Common Stock Certificate.                              (1)
         10.15       Employment Agreement of Barry M. Sherman, M. D.
         10.16       1996 Stock Plan and form of agreement.
         27.1        Financial Data Schedule
</TABLE>

              (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, 1996.

                                       9
<PAGE>   10
                                    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 8, 1996      By:/s/ JOHN W. VARIAN
                                  --------------------------------
                                      John W. Varian
                                      Vice President,
                                      Finance and Chief Financial  Officer
                                      on behalf of the Company and
                                      as principal financial and accounting
                                      officer



                                       10
<PAGE>   11
                                 EXHIBIT INDEX

EXHIBIT         DESCRIPTION                                             PAGE
-------         -----------                                             ----
3.1             Restated and Amended Articles of Incorporation          (1)
3.2             Bylaws, as amended.                                     (1)
4.1             Form of Common Stock Certificate.                       (1)
10.15           Employment Agreement of Barry M. Sherman, M.D.
10.16           1996 Stock Plan and form of agreement.
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.