<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 March 31, 2000, or

[   ] Transition Period Pursuant to Section 13 or 15(d) of the Securities
      Exchange Act of 1934 for the Transition Period From ______ to ______ .

                         Commission file number 0-19591

                                  EPIMMUNE INC.
             (Exact name of Registrant as specified in its charter)


                Delaware                             33-0245076
        ------------------------                 -------------------
        (State of Incorporation)                  (I.R.S. Employer
                                                 Identification No.)

                             5820 Nancy Ridge Drive
                           San Diego, California 92121
                    (Address of principal executive offices)

                                 (858) 860-2500
                         (Registrant's telephone number)

Indicate by check mark whether the Registrant (1) has filed all reports 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

Indicate the number of shares outstanding of each of the issuer's classes of
common stock, as of the latest practicable date.

Common Stock:  $.01 par value 7,344,764 shares outstanding as of April 30, 2000.


                                       1
<PAGE>   2

                                  EPIMMUNE INC.
                                QUARTERLY REPORT
                                    FORM 10-Q

                                TABLE OF CONTENTS

<TABLE>
<S>                                                                                         <C>
COVER PAGE.................................................................................   1

TABLE OF CONTENTS..........................................................................   2

PART I.  FINANCIAL INFORMATION

         ITEM 1.    Financial Statements

                    Condensed Consolidated Balance Sheets as of
                    March 31, 2000 and December 31, 1999...................................   3

                    Condensed Consolidated Statements of Operations
                    For the Three Months Ended March 31, 2000 and 1999.....................   4

                    Condensed Consolidated Statements of Cash Flows
                    For the Three Months Ended March 31, 2000 and 1999.....................   5

                    Notes to Condensed Consolidated Financial Statements...................   6

         ITEM 2.     Management's Discussion and Analysis of Financial
                     Condition and Results of Operations...................................   9

         ITEM 3.     Quantitative and Qualitative Disclosures about Market Risk............   *

PART II. OTHER INFORMATION

         ITEM 1.    Legal Proceedings......................................................   *

         ITEM 2.    Changes in Securities and Use of Proceeds..............................  19

         ITEM 3.    Defaults upon Senior Securities........................................   *

         ITEM 4.    Submission of Matters to a Vote of Security Holders....................   *

         ITEM 5.    Other Information......................................................   *

         ITEM 6.    Exhibits and Reports on Form 8-K.......................................  19

         SIGNATURE.........................................................................  20
</TABLE>

* No information provided due to inapplicability of item.


                                       2
<PAGE>   3

PART I. FINANCIAL INFORMATION
ITEM I. FINANCIAL STATEMENTS


                                  EPIMMUNE INC.
                      CONDENSED CONSOLIDATED BALANCE SHEETS
                        (IN THOUSANDS, EXCEPT SHARE DATA)

<TABLE>
<CAPTION>
                                                         MARCH 31,     DECEMBER 31,
                                                           2000            1999
                                                        ----------     ------------
ASSETS                                                  (unaudited)
<S>                                                      <C>           <C>
Current assets:
  Cash and cash equivalents                              $   4,187       $   1,843
  Short-term investments                                     7,436           6,412
  Prepaids and other current assets                            654             460
                                                         ---------       ---------
    Total current assets                                    12,277           8,715

Restricted cash                                                472             472
Property and equipment, net                                    851             817
Patents and other assets                                     2,726           2,701
                                                         ---------       ---------
                                                         $  16,326       $  12,705
                                                         =========       =========

LIABILITIES AND STOCKHOLDERS' EQUITY
Current liabilities:
  Accounts payable and accrued liabilities               $   1,054       $     970
  Deferred contract revenues                                    44              38
  Accrued restructuring cost                                   253             342
  Accrued payroll and related expenses                         253             212
  Current portion of notes payable                             236             230
                                                         ---------       ---------
    Total current liabilities                                1,840           1,792

Notes payable, less current portion                            374             436
Deferred rent                                                   74              55

Commitments

Stockholders' equity:
  Preferred stock, $.01 par value, 10,000,000
    shares authorized, 1,409,288 shares issued
    and outstanding at March 31, 2000  and                      14              14
    December 31, 1999
  Common stock, $.01 par value, 25,000,000 shares
    authorized, 7,344,764 shares and 6,048,945
    shares issued and outstanding at March 31, 2000
    and December 31, 1999, respectively                         73              60
  Additional paid-in capital                               151,707         147,393
  Accumulated deficit                                     (137,702)       (136,988)
  Unrealized loss on available-for-sale securities             (54)            (57)
                                                         ---------       ---------
       Total stockholders' equity                           14,038          10,422
                                                         ---------       ---------
                                                         $  16,326       $  12,705
                                                         =========       =========
</TABLE>

See accompanying notes.


                                       3
<PAGE>   4

                                  EPIMMUNE INC.
                 CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS
                                   (UNAUDITED)
                      (IN THOUSANDS, EXCEPT PER SHARE DATA)

<TABLE>
<CAPTION>
                                                               THREE MONTHS ENDED MARCH 31,
                                                              -----------------------------
                                                                 2000              1999
                                                              -----------       -----------
<S>                                                           <C>              <C>
REVENUES
  Research and development                                          $   -       $       500
  Research grants                                                     328               429
                                                              -----------       -----------
Total revenues                                                        328               929

COST AND EXPENSES
  Research and development                                          1,478             4,279
  General and administrative                                          661             1,238
  Restructuring costs                                                   -             3,700
                                                              -----------       -----------
Total costs and expenses                                            2,139             9,217
                                                              -----------       -----------
Loss from operations                                               (1,811)           (8,288)

Minority interest in net loss of consolidated subsidiary                -               141
Interest income, net                                                  136               103
Other income, net                                                     961             3,296
                                                              -----------       -----------
Net loss                                                      $      (714)      $    (4,748)
                                                              ===========       ===========
Net loss per share - basic and diluted                        $     (0.11)      $     (0.95)
                                                              ===========       ===========
Shares used in computing net loss per share - basic
and diluted                                                     6,276,335         4,991,531
                                                              ===========       ===========
</TABLE>


See accompanying notes.


                                       4
<PAGE>   5

                                  EPIMMUNE INC.
                 CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS
                                   (UNAUDITED)
                                 (IN THOUSANDS)

<TABLE>
<CAPTION>
                                                            THREE MONTHS ENDED MARCH 31,
                                                            ----------------------------
                                                                2000           1999
                                                               -------       -------
<S>                                                         <C>           <C>
OPERATING ACTIVITIES

Net loss                                                       $  (714)      $(4,748)
Adjustments to reconcile net loss to net cash used in
  operating activities:
  Depreciation and amortization                                    125           179
  Deferred rent                                                     19            --
  Deferred revenue                                                   6          (515)
  Gain on disposal of assets                                        (5)       (3,296)
  Minority interest in consolidated subsidiary                      --          (141)
  Accrued restructuring                                             --         3,700
  Restructuring operating expenses                                 (89)           --
  Changes in operating assets and liabilities
    Other current assets                                          (194)          992
    Accounts payable and accrued liabilities                        84         1,076
    Accrued payroll and related expenses                            41           (87)
                                                               -------       -------
Net cash used in operating activities                             (727)       (2,840)

INVESTING ACTIVITIES
Purchases of available-for-sale securities                      (2,150)       (1,963)
Maturities of available-for-sale securities                      1,129           967
Sales of available-for-sale securities                              --         1,108
Proceeds from sale of property and equipment                         5         3,195
Proceeds from the sale of patents (net of fees)                     --         2,914
Purchase of property and equipment                                 (83)         (282)
Patents                                                           (101)           --
Deposits and other assets                                           --            10
                                                               -------       -------
Net cash (used in) provided by investing activities             (1,200)        5,949

FINANCING ACTIVITIES
Principal payments under equipment notes payable and note
payable to bank                                                    (56)         (110)
Net proceeds from issuance of common stock                       4,327           194
                                                               -------       -------
Net cash provided by financing activities                        4,271            84
Increase in cash and cash equivalents                            2,344         3,193
Cash and cash equivalents at beginning of year                   1,843         2,594
                                                               -------       -------
Cash and cash equivalents at end of period                     $ 4,187       $ 5,787
                                                               =======       =======
SUPPLEMENTAL DISCLOSURE OF CASH FLOW INFORMATION
Interest paid                                                  $    16       $    69
                                                               =======       =======
SUPPLEMENTAL DISCLOSURES OF NON-CASH INVESTING AND
FINANCING ACTIVITIES
Unrealized gains(losses) on available-for-sale securities      $     3       $   (32)
                                                               =======       =======
Asset write down in accrued restructuring charge               $    --       $   736
                                                               =======       =======
Assumption of debt                                             $    --       $   868
                                                               =======       =======
Deferred compensation                                          $    36       $    --
                                                               =======       =======
</TABLE>

See accompanying notes.


                                       5
<PAGE>   6

                                  EPIMMUNE INC.
              NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS
                                   (UNAUDITED)
                                 MARCH 31, 2000

1. BASIS OF PRESENTATION

The interim unaudited condensed consolidated financial statements contained
herein have been prepared in accordance with generally accepted accounting
principles for interim financial information. Accordingly, they do not include
all of the information and footnotes required by generally accepted accounting
principles for complete financial statements. In management's opinion, the
unaudited information includes all adjustments, consisting only of normal
recurring adjustments, necessary for a fair presentation of the financial
position, results of operations and cash flows for the periods presented.
Interim results are not necessarily indicative of results to be expected for the
full year. The financial statements should be read in conjunction with the
audited consolidated financial statements and footnotes thereto included in the
Company's Form 10-K for the year ended December 31, 1999.

Unless otherwise indicated, all references to "Cytel" are to predecessor Cytel
Corporation, and all references to "Epimmune" are to Epimmune Inc., a
majority-owned subsidiary of Cytel until July 1, 1999, at which time Cytel and
Epimmune merged. All references to the "Company" are to the combined entity of
Cytel and Epimmune.

On July 1, 1999, the Company completed a series of transactions (the "Exchange
Transactions") in which it: (i) transferred all of the outstanding shares of
Epimmune's Series B-1 Preferred Stock then held by Cytel to G.D.Searle & Co.
("Searle") in exchange for all of the outstanding shares of Cytel's Series B
Preferred Stock, (ii) issued 859,666 shares of Cytel's Series S Preferred Stock
and 549,622 shares of Cytel's Series S-1 Preferred Stock to Searle in exchange
for all outstanding shares of Epimmune's Series B Preferred Stock and Series B-1
Preferred Stock and (iii) issued a total of 1,027,782 shares of Cytel's Common
Stock to the holders of Common Stock of Epimmune in exchange for all outstanding
shares of Epimmune's Common Stock. The acquisition of the minority interest in
Epimmune, through the exchange transaction, was accounted for as a purchase. The
Company recorded the acquisition of the minority interest at the fair market
value of the preferred and common stock issued, and determined that the excess
of the purchase price over the identifiable net assets of $3.2 million was
in-process technology based on a discounted cash flow analysis of that
technology. The analysis, with a discount rate of 50%, was based on estimated
research and development costs for nine years and product revenues beginning in
year six, after the assumed completion of clinical trials and product approval
by the FDA. The analysis also considered milestone payments based on scientific
accomplishments and new collaborative revenues based on projected future
collaboration agreements. The value of the technology was charged to acquired
in-process technology because technological feasibility had not been achieved
nor had alternative future uses for the technology been identified. Following
the Exchange Transactions, Cytel merged with Epimmune and changed its name to
Epimmune Inc. As of March 31, 2000, Searle owned 4.32% of the Company's
outstanding common stock and all of the Company's outstanding preferred stock.

Prior year condensed consolidated financial statements include the accounts of
Cytel and Epimmune, a majority-owned subsidiary Epimmune. All significant
intercompany accounts and transactions have been eliminated in consolidation.
The minority interest calculation was based on the average quarterly third
parties' ownership in Epimmune.


                                       6
<PAGE>   7

Basic and diluted net loss per share is computed using the weighted average
number of common shares outstanding during the period, excluding owned but
unvested shares. All potential common shares have been excluded from the diluted
net loss per share calculations, as they are antidilutive.

2. NEW ACCOUNTING STANDARD

In June 1998, the Financial Standards Accounting Board, or FASB, issued SFAS No.
133, Accounting for Derivative Instruments and Hedging Activities, which
establishes accounting and reporting standards for derivative instruments and
hedging activities. The Statement will require the recognition of all
derivatives on our balance sheet at fair value. The FASB subsequently delayed
implementation of the standard for the financial years beginning after June 15,
2000. We expect to adopt the new Statement effective January 1, 2001. The impact
on our financial statements is not expected to be material.

3. DISCONTINUANCE OF CYTEL OPERATIONS

In the first quarter of 1999, Cytel discontinued its therapeutic
anti-inflammatory business and recorded a restructuring charge of $3.7 million,
an amount that was reduced to $2.7 million in the fourth quarter of 1999. At the
end of the first quarter 2000, the balance of the restructuring charge is $0.3
million. The accrued restructuring charge includes the following:

<TABLE>
<CAPTION>
                                              March 31,   December 31,
                                                2000         1999
                                              ---------   ------------
<S>                                           <C>         <C>
Minimum commitments for lease facilities      $     --      $ 56,000
Employee severance                              10,000        10,000
Other loss contingencies                       243,000       276,000
                                              --------      --------
Accrued restructuring costs                   $253,000      $342,000
</TABLE>

4. SALE OF CYTEL ASSETS

In the first quarter of 1999, Cytel completed two transactions related to the
sale of its Glytec carbohydrate synthesis and manufacturing business. One
transaction included the sale of fixed assets and intellectual property, and
assignment of certain liabilities and transfer of certain personnel relating to
the Glytec business to Baxter Healthcare Corporation's Nextran Unit. The other
transaction included the sale of intellectual property to  Neose Technologies,
Inc. ("Neose"). Cytel recorded a gain of approximately $3.3 million in
connection with the two transactions. In addition, Neose paid an additional $1.5
million into escrow, the release of which is conditioned on the resolution of
certain matters relating to the patents and licenses acquired by Neose, and may
pay us up to an additional $1.6 million contingent on potential payments and
revenues realized by Neose in connection with certain future corporate
collaborations. On March 29, 2000, $0.5 million was released from escrow to the
Company based on the satisfaction of certain escrow requirements under the
agreement.

5. ELAN

On March 7, 2000, the Company received a $0.5 million payment from Elan for the
assignment of a license agreement to which Cytel was a party. We retained an
option for a non-exclusive license to certain technology.

6. PRIVATE PLACEMENT

On February 16, 2000, the Company completed a private placement of 1,200,000
newly issued shares of common stock at $3.60 per share, raising proceeds of $4.3
million.


                                       7
<PAGE>   8

7. SUBSEQUENT EVENT

On April 26, 2000, the Company signed a modification to an existing loan
agreement with Silicon Valley Bank for $0.4 million. These funds will primarily
be used for enhancements and upgrades of our scientific information management
systems and databases.


                                       8
<PAGE>   9

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

Except for the historical information contained herein, the following discussion
contains forward-looking statements that involve risks and uncertainties. Our
actual results could differ materially from those discussed here. Factors that
could cause or contribute to such differences include, without limitation, those
discussed below and in the section entitled "Risks and Uncertainties", as well
as those discussed in the Company's Annual Report on Form 10-K for the fiscal
year ended December 31, 1999.

Unless otherwise indicated, all references to "Cytel" are to Cytel Corporation.
Epimmune Inc. was a majority-owned subsidiary of Cytel until July 1, 1999, at
which time Cytel and Epimmune Inc. merged. All references to "we," "us" or "our
company" are to the combined entity of Cytel and Epimmune Inc.

Since Cytel's inception in July 1987, we have devoted substantially all of our
resources to the discovery and development of potential therapeutic and
prophylactic products. To date, we have not received any revenues from the sale
of products. We have funded our research and development primarily from
equity-derived working capital and through strategic alliances with other
companies. We have been unprofitable since our inception and expect to incur
substantial operating losses for the next several years. As of March 31, 2000,
our accumulated deficit was approximately $137.7 million.


                                       9
<PAGE>   10

RESULTS OF OPERATIONS

Three months ended March 31, 2000 ("2000"), as compared with three months ended
March 31, 1999 ("1999").

In 2000, we had total revenues of $0.3 million from research grants, as compared
to $0.9 million in 1999, which included $0.5 million of revenue recognized in
connection with the sale of Cytel's Glytec carbohydrate synthesis and
manufacturing business.

In 2000, research and development expenses decreased to $1.5 million from $4.3
million in 1999. The decrease relates to the discontinuation of Cytel operations
during the first quarter of 1999. General and administrative expenses decreased
to $0.7 million in 2000 from $1.2 million in 1999. This decrease also relates to
the discontinuation of Cytel's operations.

The restructuring charge of $3.7 million recorded in 1999 relates to the
termination of non-Epimmune operations. We also recorded a gain of $3.3 million
on disposal of assets in 1999 related to the sale of Cytel's Glytec carbohydrate
synthesis and manufacturing business. In 2000, other income was $1.0 million,
representing a payment from Elan of $0.5 million and release of $0.5 million
from escrow under the Neose agreement.

Net interest income was $0.1 million in 2000 and 1999, based on comparable
average cash balances.

We expect to incur operating losses over the next several years due to
continuing expenses associated with our research and development programs,
including preclinical testing and clinical trials. Operating losses may
fluctuate from quarter to quarter as a result of differences in the timing of
revenues received and expenses incurred, and such fluctuations may be
substantial.

LIQUIDITY AND CAPITAL RESOURCES

The following discussion reflects financial information for Cytel and Epimmune
on a consolidated basis.

We have financed operations since inception primarily through private placements
of our equity securities, two public common stock offerings, revenues under
collaborative research and development agreements, grant revenues, capital and
operating lease transactions, certain asset divestitures and interest income.
Through March 2000, we have raised approximately $149.5 million from the sale of
equity securities.

In February 2000, we raised $4.3 million through the private placement of an
aggregate of 1.2 million shares of our common stock. The purchase price was
$3.60 per share, representing a 15% discount to the prior 30-day trading average
for our common stock. As of March 31, 2000, we had approximately 8,811,141
shares outstanding on an as-converted basis, assuming conversion of preferred
shares held by Pharmacia Corporation (formerly known as G.D. Searle, a
wholly-owned subsidiary of Monsanto Company). Investors in the private placement
included the State of Wisconsin Investment Board and the Biotechnology Value
Fund, L.P. and related funds.


                                       10
<PAGE>   11

As of March 31, 2000, our cash, cash equivalents, restricted cash and short-term
investments were $12.1 million compared to $8.7 million at December 31, 1999.
The increase was primarily due to private placement proceeds of $4.3 million
partially offset by cash used for operations. We expect to continue to use our
cash, cash equivalents and short-term investments to fund our ongoing vaccine
research programs. We had net working capital of $10.4 million as of March 31,
2000 compared to $6.9 million as of December 31, 1999.

Capital expenditures totaled $0.1 million in the first quarter 2000 compared to
$0.3 million in the first quarter 1999. Expenditures, during both periods, were
primarily for laboratory equipment. On April 26, 2000, we signed a modification
to an existing loan agreement with Silicon Valley Bank for an additional $0.4
million to be utilized in 2000. These funds will primarily be used for
enhancements and upgrades of our scientific information management systems and
databases. We have financed our laboratory equipment and research and office
facilities primarily through operating lease arrangements and a note payable.

We expect to incur substantial additional research and development expenditures,
including costs related to preclinical testing, clinical trials and
manufacturing, as well as marketing and distribution expenses. It is our
intention to seek additional collaborative research and development
relationships with suitable corporate partners. There can be no assurance that
any agreements that may result from these discussions will successfully reduce
our funding requirements. Additional equity or debt financing will be required,
and there can be no assurance that these funds will be available on favorable
terms, if at all. If adequate funds are not available we may be required to
delay, scale back or eliminate one or more of its drug discovery or development
programs or obtain funds through arrangements with collaborative partners or
others that may require us to relinquish rights to certain of its technologies,
product candidates or products that we would not otherwise relinquish.

We expect our existing resources will be adequate to satisfy its operational
requirements through the end of 2001. The estimate for the period for which we
expect our available cash balances and existing sources of funding to be
sufficient to meet our operational requirements is a forward-looking statement
that involves risks and uncertainties as set forth herein and in our Form 10-K
for the year ended December 31, 1999.

Our future capital requirements depend on many factors, including as follows:
continued scientific progress in its drug discovery programs, the magnitude of
these programs, progress with preclinical testing and clinical trials, the time
and costs involved in obtaining regulatory approvals, the costs involved in
filing, prosecuting and enforcing patent claims, competing technological and
market developments, changes in the existing collaborative research
relationships, our ability to establish and maintain development arrangements,
the cost of manufacturing scale-up and effective commercialization activities
and arrangements.

As is typical in the biotechnology industry, our commercial success will depend
in part on neither infringing patents issued to competitors nor breaching the
technology licenses upon which the Company's products might be based. Our
business is also subject to other significant risks, including the uncertainties
associated with the lengthy regulatory approval process and with potential
competition from other products. Even if our products appear promising at an
early stage of development, they may not reach the market for a number of
reasons. Such reasons include, but are not limited to our inability to fund
clinical development of such products, or the possibilities that the potential
products will be found ineffective during clinical trials, fail to receive
necessary regulatory approvals, be difficult to manufacture on a large scale, or
be uneconomical to market.


                                       11
<PAGE>   12

RISKS AND UNCERTAINTIES

We wish to caution readers that the following important factors, among others,
in some cases have affected our results and in the future could cause our actual
results and needs to vary materially from forward-looking statements made from
time to time by us on the basis of management's then-current expectations. The
business in which we are engaged is in rapidly changing and competitive markets
and involves a high degree of risk, and accuracy with respect to forward-looking
projections is difficult.

WE ARE AT AN EARLY STAGE OF DEVELOPMENT. IF WE DO NOT SUCCESSFULLY DEVELOP AND
COMMERCIALIZE OUR PRODUCTS, WE MAY NEVER GENERATE SIGNIFICANT REVENUES.

We are a research and development focused company. In collaboration with our
corporate partner, Pharmacia, we expect that Pharmacia will initiate Phase I/II
human clinical trials by the end of 2000. There are many factors which are
outside of our control that may effect the timing of these trials and we cannot
assure you the trials will commence within the anticipated timeframe. We have
not completed the development of any product and, accordingly, have not begun to
market or generate revenues from the commercialization of any product. We do not
expect to market any of our therapeutic or prophylactic products for a number of
years. If we do not successfully develop and commercialize products we may never
generate significant revenues. Our potential therapies under development will
require time consuming and costly research and development efforts, preclinical
studies, clinical testing, regulatory approvals and additional investment prior
to their commercialization, which may never occur.

We cannot guarantee that our research and development programs will be
successful or that we can show that our products are safe and effective in
humans. For example, in March 1999, Cytel completed its Phase II/III clinical
trial of Cylexin, its lead cell adhesion inhibitor compound. Based on
disappointing results from this Phase II/III clinical trial, Cytel decided to
terminate the clinical trials of Cylexin and discontinue its therapeutic
anti-inflammatory business. Unacceptable toxicities or side effects may occur at
any time in the course of human clinical trials or during commercial use. Delays
in planned patient enrollment in our clinical trials may result in increased
costs, program delays or both. The appearance of any unacceptable toxicities or
side effects could interrupt, limit, delay or abort the development of any of
our products or, if previously approved, necessitate their withdrawal from the
market.

We may never obtain FDA or other necessary regulatory approvals to successfully
commercialize any of our products under development. Further, we may not be able
to manufacture any products in commercial quantities in compliance with
regulatory requirements at an acceptable cost. Even if we successfully develop
and obtain approval for our products, we may fail to achieve the necessary
market acceptance of these products. Our failure to address problems and delays
relating to research and development, regulatory approval, manufacturing and
marketing would harm our business.

IF PHARMACIA TERMINATES ITS COLLABORATION WITH US OR FAILS TO PERFORM AS
EXPECTED UNDER THE COLLABORATION AGREEMENT, IT WILL SIGNIFICANTLY HARM THE
DEVELOPMENT OF OUR CANCER EPITOPE PRODUCTS.

We have entered into a research and development collaboration with Pharmacia
with respect to the production, use and sale of pharmaceutical products derived
from our cancer epitopes and the use thereof in therapeutic vaccines. This
collaboration is our only significant collaboration, and we are substantially
dependent upon it. The success of the collaboration will depend, in significant
part, on Pharmacia's development, competitive marketing and strategic
considerations, including the relative advantages of alternative products being
developed or marketed by competitors. We expect that substantially all of our
revenues for the foreseeable future will result from payments under our
existing, and any future, collaborations, including royalties on product sales
and interest income. We cannot be certain that Pharmacia will perform its
obligations under the collaboration or that we will receive any future milestone
payments or other amounts under the collaboration.


                                       12
<PAGE>   13

We do not directly control the amount or timing of resources that Pharmacia will
devote to our collaboration, including the decision whether to proceed with
clinical trials. Pharmacia may not commit sufficient resources to our research
and development programs or the commercialization of our products. If Pharmacia
fails to conduct its activities in a timely manner, or at all, our preclinical
or clinical development related to our partnership with Pharmacia could be
delayed or terminated. The suspension or termination of the our collaboration
with Pharmacia, the failure of such collaboration to be successful or the delay
in the development or commercialization of pharmaceutical products pursuant to
such collaboration could harm our business.

IF WE CANNOT OBTAIN COLLABORATION OR LICENSE AGREEMENTS ON ACCEPTABLE TERMS IN
THE FUTURE, WE MAY NOT SUCCESSFULLY DEVELOP SOME OF OUR PRODUCTS.

We expect to rely on collaborative arrangements both to develop and
commercialize pharmaceutical products. We cannot be certain that we will be able
to enter into collaborative arrangements in the future, that any such
arrangements will be successful or that we will receive royalty revenues,
license fees or milestone payments from any such collaborative arrangements. In
addition, our collaborative partners may pursue alternative technologies or
develop alternative compounds either on their own or in collaboration with
others as a means of developing treatments for the disease targeted by any
collaborative program with us. In addition, we may be required to enter into
licenses or other collaborative agreements with third parties in order to access
technologies that are necessary to successfully develop certain of our products.
We cannot be certain that we will be able to successfully negotiate acceptable
licenses or other collaborative arrangements that will allow us to access such
technologies. In addition, we cannot be certain that any technologies accessed
through such licenses or other collaborations will successfully meet our
requirements.

OUR ADDITIONAL FINANCING REQUIREMENTS AND LIMITED ACCESS TO FINANCING MAY
ADVERSELY AFFECT OUR ABILITY TO DEVELOP PRODUCTS.

As of March 31, 2000, we had $12.1 million in cash, cash equivalents, restricted
cash and short-term investments. Our future capital requirements will depend on
many factors, including as follows: our ability to establish and maintain
collaborative arrangements; progress with pre-clinical testing and clinical
trials; the time and costs involved in obtaining regulatory approvals; the costs
involved in filing, prosecuting and enforcing patent claims; competing
technological and market developments; changes in our existing research
relationships; continued scientific progress in our drug discovery programs; the
magnitude of our drug discovery programs; the cost of manufacturing scale-up;
and effective commercialization activities and arrangements.

We intend to seek additional funding through collaborative arrangements or
equity or debt financings. If additional financing is not available, we
anticipate that our existing resources will enable us to maintain our current
and planned operations through the end of 2001. We may not be able to obtain
financing on favorable terms, if at all, or enter additional collaborations to
reduce our funding requirements. If we acquire funds by issuing securities,
further dilution to existing stockholders may result. If we acquire funds
through additional collaborations, we will likely have to relinquish some or all
of the rights to products or technologies that we may have otherwise developed
ourselves.

OUR HISTORY OF OPERATING LOSSES AND OUR EXPECTATIONS OF CONTINUING LOSSES MAY
HURT OUR ABILITY TO CONTINUE OPERATIONS.

We have experienced significant operating losses since our inception in 1987. As
of March 31, 2000, we had an accumulated deficit of $137.7 million. We have not
generated revenues from the commercialization of any product. All of our
revenues to date have consisted of contract research and


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development revenues, license and milestone payments, research grants, certain
asset divestitures and interest income. We expect to incur substantial net
operating losses which may imperil our ability to continue operations. To
achieve profitable operations, we, alone or with partners, must successfully
identify, develop, register and market proprietary products. We may not be able
to generate sufficient product revenue to become profitable on a sustained basis
or at all.

IF WE CANNOT COST-EFFECTIVELY MANUFACTURE OUR PRODUCTS AND THE PRODUCTS OF OUR
PARTNERS IN COMMERCIAL QUANTITIES AND IN COMPLIANCE WITH REGULATORY
REQUIREMENTS, WE MAY NOT BE ABLE TO SUCCESSFULLY COMMERCIALIZE OUR PRODUCTS.

To be successful, our products and the products of our partners must be
manufactured in commercial quantities in compliance with regulatory requirements
and at an acceptable cost. We have not commercialized any products, nor have we
demonstrated that we can manufacture commercial quantities of our product
candidates or our partners' product candidates in accordance with regulatory
requirements. If we cannot manufacture products in suitable quantities in
accordance with regulatory standards, either on our own our through contracts
with third parties, it may delay clinical trials, regulatory approvals and
marketing efforts for such products. Such delays could adversely affect our
competitive position and our chances of achieving profitability. We cannot be
sure that we can manufacture, either on our own our through contracts with third
parties, such products at a cost or in quantities which are commercially viable.

THE LENGTHY APPROVAL PROCESS AND UNCERTAINTY OF GOVERNMENT REGULATORY
REQUIREMENTS MAY DELAY OR PREVENT US FROM COMMERCIALIZING PRODUCTS.

We cannot commercialize our products if we do not receive FDA or foreign
approval for our products. Clinical testing, manufacture, promotion and sale of
our products are subject to extensive regulation by numerous governmental
authorities in the United States, principally the FDA, and corresponding state
and foreign regulatory agencies. These regulations may delay or prevent us from
commercializing products. Noncompliance with applicable requirements can result
in, among other things, fines, injunctions, seizure of products, total or
partial suspension of product marketing, failure of the government to grant
premarket approval, withdrawal of marketing approvals and criminal prosecution.

The regulatory process for new therapeutic drug products, including the required
preclinical studies and clinical testing, is lengthy and expensive. We may not
receive necessary FDA or foreign clearances for any of our potential products in
a timely manner, or at all. The length of the clinical trial process and the
number of patients the FDA will require to be enrolled in the clinical trials in
order to establish the safety and efficacy of our products is uncertain. The FDA
or Epimmune and its collaborators may decide to discontinue or suspend clinical
trials at any time if the subjects or patients who are participating in such
trials are being exposed to unacceptable health risks or if the results show no
or limited benefit in patients treated with the drug compared to patients in the
control group.

We may encounter significant delays or excessive costs in our efforts to secure
necessary approvals. Regulatory requirements are evolving and uncertain. Future
United States or foreign legislative or administrative acts could also prevent
or delay regulatory approval of our products. We may not receive the necessary
approvals for clinical trials, manufacturing or marketing of any of our products
under development. Even if we obtain commercial regulatory approvals, the
approvals may significantly limit the indicated uses for which we may market our
products. In addition, the FDA may continually review a product after its
initial approval and commercialization. Later discovery of previously unknown
problems or failure to comply with the applicable regulatory requirements may
result in restrictions on the marketing of a product or withdrawal of the
product from the market, as well as possible civil or criminal sanctions.


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<PAGE>   15

To market any drug products outside of the United States, we are also subject to
numerous and varying foreign regulatory requirements, implemented by foreign
health authorities, governing the design and conduct of human clinical trials
and marketing approval. The approval procedure varies among countries and can
involve additional testing, and the time required to obtain approval may differ
from that required to obtain FDA approval. The foreign regulatory approval
process includes all of the risks associated with obtaining FDA approval set
forth above, and approval by the FDA does not ensure approval by the health
authorities of any other country, nor does the approval by foreign health
authorities ensure approval be the FDA.

Among the other requirements for regulatory approval is the requirement that
prospective manufacturers conform to the FDA's Good Manufacturing Practices,
GMP, requirements specifically for biological drugs, as well as for other drugs.
In complying with the FDA's GMP requirements, manufacturers must continue to
expend time, money and effort in production, record keeping and quality control
to assure that the product meets applicable specifications and other
requirements. Failure to comply with the FDA's GMP requirements subjects the
manufacturer to possible FDA regulatory action. If we or our contract
manufacturers, if any, fail to maintain compliance with the FDA's GMP
requirements on a continuing basis, it could materially adversely affect our
operations, commercialization efforts and profitability.

TECHNOLOGICAL CHANGE AND COMPETITION MAY RENDER OUR POTENTIAL PRODUCTS OBSOLETE.

The biotechnology industry continues to undergo rapid change and competition is
intense and is expected to increase. Our competitors may succeed in developing
technologies and products that are more effective or affordable than any of the
products we are developing or which would render our technology and products
obsolete and noncompetitive. We compete with many public and private companies,
including pharmaceutical companies, chemical companies, specialized
biotechnology companies and academic institutions. Many of our competitors have
substantially greater experience, financial and technical resources and
production, marketing and development capabilities than us. In addition, many of
our competitors have significantly greater experience conducting preclinical
studies and clinical trials of new products, and in obtaining regulatory
approvals for such products. Accordingly, some of our competitors may succeed in
obtaining developing and commercializing products more rapidly or effectively
than us, or in developing technology and products that would render our
technology and products obsolete or noncompetitive. We are aware of companies
that are pursuing the development of novel pharmaceuticals which target the same
diseases that we are targeting. These and other efforts by potential competitors
may be successful, and other technologies may be developed to compete with our
technologies. If we cannot successfully respond to technological change in a
timely manner, our commercialization efforts may be harmed.

Our products under development address a range of markets. Our competition will
be determined in part by the potential indications for which our compounds are
developed and ultimately approved by regulatory authorities. For certain of our
potential products, an important factor in competition may be the timing of
market introduction of our products and competitive products. Accordingly, the
relative speed with which we can develop products, complete the clinical trials
and approval processes and supply commercial quantities of the products to the
market are expected to be important competitive factors. We expect that
competition among products approved for sale will be based, among other things,
on product effectiveness, safety, reliability, availability, price and patent
position.

OUR FAILURE TO OBTAIN ISSUED PATENTS AND, CONSEQUENTLY, TO PROTECT OUR
PROPRIETARY TECHNOLOGY, COULD IMPAIR OUR COMPETITIVE POSITION.

Our success will depend in part on our ability to obtain patent protection for
our products and processes, both in the United States and other countries. The
patent position of biotechnology and pharmaceutical


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<PAGE>   16

companies is highly uncertain and involves complex legal and factual questions.
There is no consistent policy regarding the breadth of claims allowed in
biotechnology patents. We intend to file applications and pursue patent
prosecution as appropriate for patents covering both our products and processes.
We cannot be sure that patents will issue from any of the patent applications
that we own or license or that, if patents do issue, that claims allowed will be
sufficiently broad to protect our products and processes. In addition, we cannot
be certain that third parties will not challenge, invalidate or circumvent any
patents issued to us, or that the rights granted under the patents will provide
proprietary protection to us.

We also protect our proprietary technology and processes in part by
confidentiality agreements with our collaborative partners, employees and
consultants. We cannot be certain that our collaborative partners, employees and
consultants will not breach these agreements, that we will have adequate
remedies for any breach, or that our trade secrets will not otherwise become
known or be independently discovered by competitors.

WE MAY NOT BE ABLE TO COMMERCIALIZE OUR OTHER PRODUCTS UNDER DEVELOPMENT IF THEY
INFRINGE EXISTING PATENTS OR PATENTS THAT HAVE NOT YET ISSUED, WHICH WOULD
MATERIALLY HARM OUR BUSINESS.

As is typical in the biotechnology industry, our commercial success will depend
in part on our ability to avoid infringing patents issued to competitors or
breaching the technology licenses upon which we might base our products. If we
fail to obtain a license to any technology that we require to commercialize our
products, or to develop an alternative compound and obtain FDA approval within
an acceptable period of time if required to do so, our business would be harmed.
Litigation, which could result in substantial costs to us, may also be necessary
to enforce any patents issued to us or to determine the scope and validity of
others' proprietary rights. In addition, we may have to participate in
interference proceedings declared by the United States Patent and Trademark
Office which could result in substantial costs to determine the priority of
inventions.

OUR FUTURE SUCCESS DEPENDS IN PART ON THE CONTINUED SERVICE OF OUR KEY
SCIENTIFIC AND MANAGEMENT PERSONNEL AND OUR ABILITY TO IDENTIFY, HIRE AND RETAIN
ADDITIONAL PERSONNEL.

We are highly dependent on the principal members of our scientific and
management staff. We do not maintain key person life insurance on the life of
any employee. Our future success also will depend in part on the continued
service of our key scientific and management personnel and our ability to
identify, hire and retain additional qualified personnel.

There is intense competition for qualified personnel in the areas of our
activities, and we cannot be sure that we will be able to continue to attract
and retain such personnel necessary for the development of our business. Because
of the intense competition, we cannot be sure that we will be successful in
adding technical personnel as needed to meet the staffing requirements of
additional collaborative relationships. Our failure to attract and retain key
personnel could be significantly detrimental to our product development programs
and could harm our business.

IF WE DO NOT DEVELOP A SUFFICIENT SALES AND MARKETING FORCE, WE MAY NOT BE ABLE
TO SUCCESSFULLY COMMERCIALIZE OUR PRODUCTS.

We have no experience in sales, marketing or distribution. Before we can market
any of our products directly, we must develop a substantial marketing and sales
force with technical expertise and supporting distribution capability.
Alternatively, we may obtain the assistance of a pharmaceutical company with a
large distribution system and a large direct sales force. Other than our
agreements with Pharmacia and Takara, we do not have any existing distribution
arrangements with any pharmaceutical company for our products under development.
We cannot be sure that we can establish sales and distribution capabilities


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<PAGE>   17

or successfully gain market acceptance for our products. If we cannot develop
sales and distribution capabilities, we may not be able to successfully
commercialize our products.

ADVERSE DETERMINATIONS CONCERNING PRODUCT PRICING, REIMBURSEMENT AND RELATED
MATTERS COULD PREVENT US FROM SUCCESSFULLY COMMERCIALIZING PRODUCTS.

Our ability to successfully commercialize our products may depend in part on the
extent to which reimbursement for the cost of such products and related
treatment will be available from government health administration authorities,
private health insurers and other organizations. Third-party payors are
increasingly challenging the price of medical products and services. Significant
uncertainty exists as to the reimbursement status of newly approved health care
products, and we cannot be certain that adequate third-party coverage will be
available to enable us to maintain price levels sufficient to realize an
appropriate return on our investment in product development. If we cannot obtain
adequate third-party coverage for our products, it could harm our business.

PRODUCT LIABILITY RISKS MAY EXPOSE US TO SIGNIFICANT LIABILITY.

Our business exposes us to potential product liability risks which are inherent
in the testing, manufacturing and marketing of human therapeutic products. While
we currently have product liability insurance, we cannot be sure that we can
maintain such insurance on acceptable terms or that our insurance will provide
adequate coverage against potential liabilities.

OUR USE OF HAZARDOUS MATERIALS COULD EXPOSE US TO SIGNIFICANT COSTS.

Our research and development processes involve the controlled storage, use and
disposal of hazardous materials, chemicals and radioactive compounds. We are
subject to federal, state and local laws and regulations governing the use,
manufacture, storage, handling and disposal of these materials and some waste
products. Although we believe that our safety procedures for handling and
disposing of these materials comply with the standards prescribed by these laws
and regulations, the risk of accidental contamination or injury from these
materials cannot be completely eliminated. In the event of an accident, we could
be held liable for any damages that result, and any liability could exceed our
resources.

Although we believe that we are in compliance in all material respects with
applicable environmental laws and regulations and currently do not expect to
make material capital expenditures for environmental control facilities in the
near term, we cannot be sure that compliance with environmental laws and
regulations in the future will not entail significant costs, or that our
business will not be harmed by current or future environmental laws or
regulations.

THE VOLATILITY OF THE PRICE OF OUR COMMON STOCK AND OUR DIVIDEND POLICY MAY HURT
OUR STOCKHOLDERS.

The market prices for securities of biotechnology companies, including our
common stock, have historically been highly volatile and currently are of new
record levels, and the market from time to time has experienced significant
price and volume fluctuations that are unrelated to the operating performance of
such companies. The following factors may have a significant effect on the
market price of our common stock:

- announcements of technological innovations or new commercial therapeutic
  products by us or others;

- governmental regulation;

- developments in patent or other proprietary rights;


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<PAGE>   18

- developments in our relationships with our collaborative partners;

- public concern as to the clinical results and/or, the safety of drugs
  developed by us or others; and

- general market conditions.


Fluctuations in financial performance from period to period also may have a
significant impact on the market price of our common stock.

THE SUBORDINATION OF OUR COMMON STOCK TO OUR PREFERRED STOCK COULD HURT COMMON
STOCKHOLDERS.

Our common stock is expressly subordinate to our Series S and Series S-1
Preferred Stock in the event of our liquidation, dissolution or winding up. If
we were to cease operations and liquidate our assets, there may not be any
remaining value available for distribution to the holders of common stock after
providing for the Series S and Series S-1 Preferred Stock liquidation
preference.

THE EFFECT OF ANTI-TAKEOVER PROVISIONS COULD ADVERSELY AFFECT OUR COMMON
STOCKHOLDERS.

Our certificate of incorporation includes a provision that requires the approval
of holders of at least 66 2/3% of our voting stock as a condition to a merger or
certain other business transactions with, or proposed by, a holder of 15% or
more of our voting stock. This approval is not required in cases where certain
of our directors approve the transaction or where certain minimum price criteria
and other procedural requirements are met. Our certificate of incorporation also
requires the approvals of holders of at least 66 2/3% of our voting stock to
amend or change the provisions mentioned relating to the transaction approval.
Finally, our certificate of incorporation provides that any action required or
permitted to be taken by our stockholders must be effected at a duly called
annual or special meeting rather than by any consent in writing.

Further, pursuant to the terms of our stockholder rights plan, we have
distributed a dividend of one right for each outstanding share of common stock.
These rights will cause substantial dilution to the ownership of a person or
group that attempts to acquire us on terms not approved by the Board of
Directors and may have the effect of deterring hostile takeover attempts.

Concentration of ownership among our existing officers, directors and principal
stockholders may prevent other stockholders from influencing significant
corporate decisions and depress our stock price.

Our officers, directors and stockholders with at least 10% of our stock together
control approximately 46% of our outstanding common stock and preferred stock,
on a combined, as-converted basis. If these officers, directors and principal
stockholders act together, they will be able to exert a significant degree of
influence over our management and affairs and over matters requiring stockholder
approval, including the election of directors and approval of mergers or other
business combination transactions. The interests of this concentration of
ownership may not always coincide with our interests or the interests of other
stockholders. For instance, officers, directors and principal stockholders,
acting together, could cause us to enter into transactions or agreements that we
would not otherwise consider. Similarly, this concentration of ownership may
have the effect of delaying or preventing a change in control of our company
otherwise favored by our other stockholders. This concentration of ownership
could depress our stock price.

WE HAVE NEVER PAID DIVIDENDS.

We have never paid any cash dividends and do not anticipate paying cash
dividends in the foreseeable future.


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PART II. OTHER INFORMATION
ITEM 2.  CHANGES IN SECURITIES AND USE OF PROCEEDS

During the period covered by this Form 10-Q, the Company sold and issued the
following securities which were registered under the Securities Act of 1933, as
amended (the "Securities Act"):

        1.     In February 2000, pursuant to the terms of an equity financing,
               we issued 1,200,000 shares of common stock to accredited
               investors at a purchase price of $3.60 per share. Gross proceeds
               to us for such financing totaled $4.3 million.

The sale and issuance of securities in the transaction described above was
deemed to be exempt from registration under the Securities Act by virtue of
Section 4(2) and/or Regulation D promulgated thereunder.

ITEM 6. EXHIBITS

        Exhibit 27.1    Financial Data Schedule


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                                  EPIMMUNE INC.

                                    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.


                                      EPIMMUNE INC.



Date: May 12, 2000                    By:     /s/ Deborah A. Schueren
                                         ---------------------------------
                                          Deborah A. Schueren
                                          President, Chief Executive Officer and
                                          Chief Financial Officer






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