<PAGE>   1
                     U.S. SECURITIES AND EXCHANGE COMMISSION
                              Washington D.C. 20549

                                   FORM 10-QSB

(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.

[ ]  TRANSITION REPORT PURSUANT TO SECTION 13 OR 15 OF THE SECURITIES EXCHANGE
     ACT OF 1934

     FOR THE TRANSITION PERIOD FROM ______________ TO ______________.


                         Commission file number 0-22170


                           EPOCH PHARMACEUTICALS, INC.
--------------------------------------------------------------------------------
        (Exact name of small business issuer as specified in its charter)


           Delaware                                              91-1311592
-------------------------------                             -------------------
(State or other jurisdiction of                              (I.R.S. Employer
incorporation or organization)                              Identification No.)

12277 134th Court N.E., Suite 110, Redmond, Washington            98052
------------------------------------------------------      -------------------
     (Address of principal executive offices)                  (Zip Code)


                                 (425) 821-7535
--------------------------------------------------------------------------------
                (Issuer's telephone number, including area code)

                                 Not Applicable
--------------------------------------------------------------------------------
              (Former name, former address and former fiscal year,
                          if changed since last report)

Check whether the issuer (1) filed all reports to be filed by Section 13 or
15(d) of the Exchange Act during the past 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
                                     ---         ---

State the number of shares outstanding of each of the issuer's classes of common
equity as of the latest practicable date.


           Class                                   Outstanding at April 13, 2000
----------------------------                       -----------------------------
Common Stock, $.01 par value                                  24,807,703

<PAGE>   2

                           EPOCH PHARMACEUTICALS, INC.

                              INDEX TO FORM 10-QSB

<TABLE>
<CAPTION>
                                                                           Page
                                                                          Number
                                                                          ------
<S>                                                                      <C>
Part I. Financial Information

     Item 1. Financial Statements

             Balance Sheets as of December 31, 1999
               and March 31, 2000 (unaudited)............................    3

             Statements of Operations (unaudited) for the three
               months ended March 31, 1999 and 2000......................    4

             Statements of Cash Flows (unaudited) for the three months
               ended March 31, 1999 and 2000.............................    5

             Notes to Financial Statements (unaudited)...................    6

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

Part II. Other Information

     Item 1. Legal Proceedings...........................................   13

     Item 6. Exhibits and Reports on Form 8-K............................   13

     Note: Items 2 - 5 are omitted, as they are not applicable.

Signature ...............................................................   14
</TABLE>

                                       2

<PAGE>   3

                           EPOCH PHARMACEUTICALS, INC.

                                 BALANCE SHEETS

                                     ASSETS

<TABLE>
<CAPTION>

                                                             DECEMBER 31,    MARCH 31,
                                                                1999           2000
                                                            -------------   ------------
                                                                            (UNAUDITED)
<S>                                                         <C>             <C>
Current assets:
    Cash and cash equivalents ............................  $  1,772,274    $ 18,348,084
    Receivables ..........................................        20,073         105,145
    Prepaid expenses .....................................        34,188          23,334
                                                            ------------    ------------
       Total current assets ..............................     1,826,535      18,476,563

Equipment, net ...........................................       399,705         462,612

Restricted cash ..........................................            --         595,700
Other assets .............................................        39,344          36,162
                                                            ------------    ------------

       Total assets ......................................  $  2,265,584    $ 19,571,037
                                                            ============    ============

                      LIABILITIES AND STOCKHOLDERS' EQUITY
Current liabilities:
  Accounts payable .......................................  $    102,884    $    153,372
  Other accrued liabilities ..............................       393,660         503,043
  Deferred revenue - current portion .....................       277,742         277,742
                                                            ------------    ------------
    Total current liabilities ............................       774,286         934,157

Deferred revenue .........................................     1,316,129       1,302,943

Stockholders' equity:
  Preferred stock, par value $.01; 10,000,000 shares
    authorized; no shares issued and outstanding .........            --              --
  Common stock, par value $.01; 50,000,000 shares
    authorized; issued and outstanding: 19,382,410 at
    December 31, 1999 and 24,314,511 at March 31, 2000 ...       193,824         243,145
Additional paid-in capital ...............................    61,625,990      79,949,843
Deferred compensation expense ............................      (111,874)        (99,886)
Accumulated deficit ......................................   (61,532,771)    (62,759,165)
                                                            ------------    ------------

       Total stockholders' equity ........................       175,169      17,333,937
                                                            ------------    ------------

Commitments and subsequent events

Total liabilities and stockholders' equity ...............  $  2,265,584    $ 19,571,037
                                                            ============    ============
</TABLE>

                 See accompanying notes to financial statements.

                                       3

<PAGE>   4

                           EPOCH PHARMACEUTICALS, INC.

                            STATEMENTS OF OPERATIONS
                                   (UNAUDITED)

<TABLE>
<CAPTION>
                                                       THREE MONTHS ENDED MARCH 31,
                                                     -------------------------------
                                                         1999               2000
                                                     ------------       ------------
<S>                                                  <C>                <C>
Revenue:
    Product sales .............................      $         --       $     85,200
    License fees ..............................                --             13,186
    Research contract revenue .................            95,092                 --
                                                     ------------       ------------
       Total revenue...........................            95,092             98,386

Operating expenses:
    Research and development ..................           644,601            733,740
    General and administrative ................           334,865            717,230
                                                     ------------       ------------
       Total operating expenses ...............           979,466          1,450,970
                                                     ------------       ------------

          Operating loss ......................          (884,374)        (1,352,584)

Other income (expense):
    Interest income ...........................            18,553            126,345
    Interest and financing expense ............          (230,563)              (155)
                                                     ------------       ------------
       Loss from continuing operations ........        (1,096,384)        (1,226,394)

Discontinued operations - gain on disposal of
  discontinued operations                                  40,000                 --
                                                     ------------       ------------

       Net loss ...............................      $ (1,056,384)      $ (1,226,394)
                                                     ============       ============

Loss per share from continuing
  operations - basic and diluted ..............      $      (0.07)      $      (0.06)
Income per share from discontinued
  operations - basic and diluted ..............                --                 --
                                                     ------------       ------------
Net loss per share - basic and diluted ........      $      (0.07)      $      (0.06)
                                                     ============       ============

Weighted average number of common shares
  outstanding - basic and diluted .............        14,830,435         21,518,898
</TABLE>

                 See accompanying notes to financial statements.


                                       4

<PAGE>   5

                           EPOCH PHARMACEUTICALS, INC.

                            STATEMENTS OF CASH FLOWS
                                   (UNAUDITED)

<TABLE>
<CAPTION>
                                                                   THREE MONTHS ENDED
                                                                        MARCH 31,
                                                               --------------------------
                                                                  1999           2000
                                                               -----------   ------------
<S>                                                            <C>           <C>
Cash flows from operating activities:
    Net loss ................................................. $(1,056,384)  $ (1,226,394)

    Adjustments to reconcile net loss to net cash
       provided by (used in) operating activities:
       Depreciation and amortization .........................      18,873         35,325
       Amortization of deferred financing expense ............     166,671             --
       Amortization of deferred compensation expense .........      11,988         11,988
       Changes in operating assets and liabilities:
          Receivables ........................................     (69,785)       (85,072)
          Prepaid expenses and other assets ..................      (2,455)        14,036
          Accounts payable ...................................     (84,499)        50,488
          Accrued interest on note payable to related party ..      63,703             --
          Accrued expenses for canceled relocation ...........    (287,397)            --
          Deferred revenue ...................................   2,300,000        (13,186)
          Other accrued liabilities ..........................      47,751        109,383
                                                               -----------   ------------
              Net cash provided by (used in)
                operating activities..........................   1,108,466     (1,103,432)
                                                               -----------   ------------

Cash flows from investing activities:
    Security deposit on new facilities .......................          --       (595,700)
    Acquisition of equipment .................................     (52,128)       (98,232)
                                                               -----------   ------------
       Net cash used in investing activities .................     (52,128)      (693,932)

Cash flows from financing activities:
    Proceeds from sale of common stock .......................          --     10,000,039
    Proceeds from exercise of warrants .......................          --      8,318,302
    Exercise of stock options ................................       9,506         54,833
                                                               -----------   ------------
       Net cash provided by financing activities .............       9,506     18,373,174
                                                               -----------   ------------

Net increase in cash and cash equivalents ....................   1,065,844     16,575,810
Cash and cash equivalents at beginning of period .............     658,363      1,772,274
                                                               -----------   ------------
Cash and cash equivalents at end of period ................... $ 1,724,207   $ 18,348,084
                                                               ===========   ============

Supplemental disclosure of cash flow information - cash
  payments made during the period for interest ............... $       189   $        155
                                                               ===========   ============
</TABLE>

                 See accompanying notes to financial statements.

                                       5

<PAGE>   6

                           EPOCH PHARMACEUTICALS, INC.

                          NOTES TO FINANCIAL STATEMENTS
                                 MARCH 31, 2000
                                   (UNAUDITED)

NOTE (1) BASIS OF PRESENTATION

        The unaudited financial statements have been prepared in accordance with
generally accepted accounting principles for interim financial information and
with the instructions to Form 10-QSB. Accordingly, they do not include all of
the information and footnotes required to be presented for complete financial
statements. The accompanying financial statements include all adjustments
(consisting only of normal recurring accruals) which are, in the opinion of
management, necessary for a fair presentation of the results for the interim
periods presented. Certain 1999 balances have been reclassified to conform with
the 2000 presentation.

        The financial statements and related disclosures have been prepared with
the presumption that users of the interim financial information have read or
have access to the audited financial statements for the preceding fiscal year.
Accordingly, these financial statements should be read in conjunction with the
audited financial statements and the related notes included in Epoch's 1999
Annual Report on Form 10-KSB as filed with the Securities and Exchange
Commission on March 30, 2000.

NOTE (2) NATURE OF BUSINESS

        Epoch Pharmaceuticals, Inc., doing business as Epoch Biosciences, is
developing and commercializing unique, proprietary technologies to enhance the
study of genes. Epoch scientists are applying their expertise in nucleic acid
chemistry to develop products that improve current methods of studying the
genetic sequence (genomes) of humans, animals and plants. Our technology is
based on our expertise in designing and synthesizing oligonucleotides (synthetic
DNA strands) bearing modifications that more selectively bind to and interact
with their target genes. Using our DNA technology, Epoch is developing molecular
tools and reagents for improved genetic sequence analysis.

        Previously, we discovered that we could adapt the compounds and
techniques we were developing for our gene modification therapeutic program to
several gene sequencing analysis systems currently in use or being developed by
others. Our technology has broad application potential in the developing fields
of molecular diagnostics and genomics, including the detection of infectious
diseases, inheritable diseases through prenatal testing, screening populations
to identify genetic markers that correlate with disease risk or drug response,
as well as any other genetic analysis based on DNA sequence determination.

        Our technologies are compatible with many methods and formats used to
perform genetic analysis.

NOTE (3) LOSS PER SHARE

        Basic loss per share is computed based on weighted average shares
outstanding during the reporting period and excludes any potential dilution.
Diluted loss per share reflects potential dilution from the exercise or
conversion of securities into common stock or from other contracts to issue
common stock. Our capital structure includes common stock options and common
stock warrants. At March 31, 2000, there were 1,646,166 options outstanding to
purchase the common stock of Epoch with exercise prices ranging from $0.30 to
$17.44. Also outstanding at March 31, 2000 were 2,020,590 warrants to purchase
the common stock of Epoch with exercise prices ranging from $0.50 to $2.50 per
share. At


                                       6


<PAGE>   7

March 31, 1999, there were 1,458,999 options outstanding to purchase the common
stock of Epoch with exercise prices ranging from $0.30 to $5.88. Also
outstanding at March 31, 1999 were 7,498,875 warrants to purchase the common
stock of Epoch with exercise prices ranging from $0.30 to $9.21 per share. The
assumed conversion and exercise of these securities have been excluded from the
calculation of diluted loss per share for both periods as their effect is
anti-dilutive.

NOTE (4) RESTRICTED CASH

        Restricted cash represents long-term certificates of deposit pledged
under a security agreement in lieu of a cash deposit on our new facility.

NOTE (5) SUBSEQUENT EVENTS

        In May 2000, we were approved for listing on the Nasdaq national Market
and our stock began trading on May 10, 2000 under the symbol EBIO.

        In May 2000, with approval from our board of directors, we began
operating under the name Epoch Biosciences. We will seek stockholder approval at
our annual meeting to formally change our corporate name.

        In May 2000, we announced a strategic alliance with Specialty
Laboratories to develop tests for residual leukemia. Under the agreement, Epoch
will develop probes for the assays using its minor groove binder and other
technologies. Specialty will develop and clinically validate the assays, and
offer them commercially under a license grant from Epoch.

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

        This Quarterly Report on Form 10-QSB contains certain forward-looking
statements within the meaning of Section 27A of the Securities Act of 1933 and
Section 21E of the Securities Exchange Act of 1934 and we intend that these
forward-looking statements be subject to the safe harbors created thereby. These
forward-looking statements include, without limitation, the development and
commercialization of our technology.

        The forward-looking statements included in this document are based on
current expectations that involve a number of risks and uncertainties. These
forward-looking statements are based on assumptions that our technology will
continue to be developed, and will not be replaced by new technology, that we
will retain key technical and management personnel, and that there will be no
material adverse change in our operations or business. Assumptions relating to
the foregoing involve judgments with respect to, among other things, future
technology, economic, competitive and market conditions, and future business
decisions, all of which are difficult or impossible to predict accurately and
many of which are beyond our control. Although we believe that the assumptions
underlying the forward-looking statements are reasonable, any of the assumptions
could prove inaccurate and, therefore, there can be no assurance that the
results contemplated in forward-looking statements will be realized. In
addition, our business and operations are subject to substantial risks which
increase the uncertainty inherent in these forward-looking statements. In light
of the significant uncertainties inherent in the forward-looking information
included in this document, the inclusion of information should not be regarded
as a representation by us or any other person that our objectives or plans will
be achieved.

        Future operating results may be impacted by a number of factors that
could cause actual results to differ materially from those stated herein, which
reflect management's current expectations. These factors include industry
specific factors, our ability to maintain access to external financing sources
and its financial liquidity, our ability to timely develop and produce
commercially viable products and our ability to manage expense levels.

        The following discussion of Epoch's financial condition and results of
operations should be read in conjunction with the financial statements and the
related notes thereto included elsewhere in this Quarterly Report on Form
10-QSB. Our actual results may differ significantly from the results discussed
in the forward-looking statements. Factors that might cause such a difference
include, but are not limited to, those discussed under "Certain Factors that May
Affect Our Business and Future Results".


                                       7

<PAGE>   8

                              RESULTS OF OPERATIONS

        Product Sales. Product sales represent the sale of specialty probes to
end users. The first shipment of these probes was in December 1999.

        License Fees. License fees reflect the amortization of initial payments
for the transfer of technology and know how. These amounts are amortized over
the life of the contract beginning in the fourth quarter of 1999.

        Research Contract Revenue. Research contract revenue reflects revenue
from U.S. government grants and contracts, and subcontracts. The company does
not have any active grants at this time.

        Research and Development. The increase in research and development
expenses of $89,000 over the comparable 1999 quarter is primarily the result of
Epoch's subcontracting support work on research and development to an outside
firm in 2000. These expenses totaled $58,000 in the first quarter. The
short-term contract was concluded in May 2000. Additional variations in research
and development expense are the result of normal business fluctuations.

        General and Administrative. General and administrative expenses
increased $382,000 in the quarter ended March 31, 2000 compared to the
respective prior year period. The increase in 2000 is primarily the result of:

        o   $150,000 in expenses incurred in connection with a warrant call and
            private placement completed during the quarter.

        o   An increase of $65,000 in expenditures associated with the filing of
            patents over the prior period. In the first quarter of 2000, we
            incurred $81,000 in fees toward filing patents on new technologies,
            as compared to $16,000 in the same period of 1999. We believe that
            these patents, if issued, will improve our proprietary position.
            There can be no assurance that our patent applications will result
            in further issued patents or that such issued patents will offer
            protection against competitors with similar technology.
            Additionally, there can be no assurance that any manufacture, use or
            sale of our technology or products will not infringe on patents or
            proprietary rights of others, and we may be unable to obtain
            licenses or other rights to these other technologies that may be
            required for commercialization of the proposed products.

        o   An increase over 1999 of $62,000 in compensation related to
            additional executive personnel.

        o   A rent increase of $22,000.

        o   Increased travel expense of $21,000.

        Further variances in general and administrative expenses between the
comparable quarters are the result of normal business fluctuations.

        Interest Income. Interest income in 2000 increased over the comparable
prior year period due to higher cash balances available for investment.


                                        8

<PAGE>   9

        Interest and Financing Expense. Interest and financing expense in 1999
represents the costs associated with the $3,000,000 note payable to a related
party, which was repaid in 1999.

        Gain on Disposal. The gain on disposal of discontinued operations
represents only that portion of the gain for which cash payments were received
during the reporting periods.

                         LIQUIDITY AND CAPITAL RESOURCES

        At March 31, 2000 we had operating cash and cash equivalents of
$18,348,000 and stockholder's equity of $17,334,000. We received an additional
$1,233,000 in cash from the exercise of warrants in April 2000.

        In February 2000 we received $10 million of private equity financing
from the sale of 1,428,577 shares of common stock at $7.00 per share. The $7.00
per share price was determined based upon the 20 day trailing average of the
closing price of the stock.

        In February 2000, Epoch exercised the redemption provision on
outstanding warrants, which were issued in a private placement in 1996 and a
warrant exchange in 1997, representing 3,801,812 shares of common stock.
Warrants representing approximately 3,305,570 shares of common stock were
exercised in the first quarter generating $8,264,000 in cash. An additional
493,192 warrants were exercised in April generating $1,233,000 in cash which
will be reflected in second quarter results.

        In addition to the warrant call, the exercise of other miscellaneous
warrants generated $54,000 in the first quarter.

        Management estimates that the March 31, 2000 cash balance, coupled with
the additional $1,233,000 received in April 2000 from the exercise of additional
warrants will be sufficient to operate through 2001.

        Utilizing our current cash balances coupled with anticipated revenues
from our licensing agreements, we plan to further develop and verify
applicability of our compounds and techniques in the developing fields of
molecular diagnostics and genomics and to determine how our technology may be
exploited.

        We are focused on the development of our products with the goal of
entering into additional corporate partnering arrangements to further
commercialize our technology. Our working capital requirements may vary
depending upon numerous factors including commercialization of our products, the
progress of our research and development, competitive and technological
advances, relocation expenses and other factors. We anticipate operating this
quarter with approximately 28 employees.

        Cash increased by $16,575,810 during the period primarily as a result of
the net of $10,000,000 received from the private placement and $8,318,000 from
the exercise of warrants offset by normal expenditures on operations and the
acquisition of $98,000 of capital equipment. The comparable period of the prior
year had a cash increase of $1,066,000, the net result of $2,300,000 received
from the PE Biosystems license agreement offset by normal operating expenditures
and the acquisition of $52,000 of equipment used in research and development.

        Variances in receivables, accounts payable and other accrued liabilities
in 2000 and 1999 are the result of normal business fluctuations.


                                       9


<PAGE>   10
                         NEW ACCOUNTING PRONOUNCEMENTS

        In March 2000 the SEC issued Staff Accounting Bulletin No. 101A. SAB
101A delays the effective date of Staff Accounting Bulletin No. 101, "Revenue
Recognition in Financial Statements," to the second quarter for fiscal years
beginning between December 15, 1999 and March 16, 2000. SAB 101 provides
guidance on revenue recognition and the SEC staff's views on the application of
accounting principles to selected revenue recognition issues. We will adopt the
provisions of SAB 101 in the second quarter of 2000. The interpretation of SAB
101 is currently uncertain as it relates to biotechnology companies and,
consequently, the impact on our financial statements is unknown. We are in the
process of determining the potential impact.

        In March 2000, the Financial Accounting Standards Board issued
Interpretation No. 44, "Accounting for Certain Transactions involving Stock
Compensation." Interpretation No. 44 clarifies the application of Accounting
Principles Board Opinion No. 25 and is effective July 1, 2000. Interpretation
No. 44 clarifies the definition of "employee" for purposes of applying APB 25,
the criteria for determining whether a plan qualifies as a non-compensatory
plan, the accounting consequence of various modifications to the terms of a
previously fixed stock option or award, and the accounting for an exchange of
stock compensation awards in a business combination. We do not expect the
adoption of Interpretation No. 44 to have a material impact on our financial
statements.

         CERTAIN FACTORS THAT MAY AFFECT OUR BUSINESS AND FUTURE RESULTS

History of Operating Losses; Anticipated Future Losses.

        Since our formation in 1985, we have generated limited revenues from the
sale of diagnostic products and from research and development grants. In 1995,
we sold substantially all of the then existing diagnostic assets that were used
to generate these product revenues. At the end of 1999, we had an accumulated
deficit of approximately $62 million. We expect to incur additional losses as we
expand our research and development efforts. We make no guarantee that we will
ever become profitable. We will need additional funds to continue our research
and development activities. See "Management's Discussion and Analysis of
Financial Condition and Results of Operations--Liquidity and Capital Resources."

Dependence Upon New and Unproven Technology.

        The science and technology of oligonucleotide-based products is rapidly
evolving. Our proposed products are in the discovery or early development stage.
The proposed products will require significant


                                       10


<PAGE>   11

further research, development, and testing and are subject to the risks of
failure inherent in the development of products based on innovative
technologies. We also face the risk that any or all of our proposed products
could prove to be ineffective or unsafe, be unmarketable because third parties
hold proprietary rights which prohibit us from marketing the proposed products,
or be an inferior product to products marketed by others. Accordingly, we cannot
predict whether our research and development activities will result in any
commercially viable products.

Reliance on Patent and Proprietary Technology; Risk of Patent Infringement.

        We attempt to protect our proprietary technology by relying on several
methods including United States patents. We also have international patent
applications that correspond to many of the U.S. patents and patent
applications. The issued patents and pending patent applications cover
inventions relating to the components of our core technologies. The expiration
dates of these patents range from January 2010 to June 2015. We make no
guarantee that any issued patents will provide us with significant proprietary
protection, that pending patents will be issued, or that products incorporating
the technology from our issued patents or pending applications will be free from
challenges by competitors.

        The biomedical industry has been characterized by extensive litigation
regarding patents and other intellectual property rights. We were defendants in
one such action which has been settled. Although patent and intellectual
property disputes in the biomedical area have often been settled through
licensing or similar arrangements, costs associated with such arrangements may
be substantial. Further, we make no guarantee that we will obtain necessary
licenses on satisfactory terms or at all. Accordingly, an adverse determination
in a judicial or administrative proceeding or our failure to obtain necessary
licenses could prevent us from manufacturing and selling our products. This
would substantially hurt our operating results, financial condition and
ultimately our business.

Competition and Changing Technology

        Many companies do research and development and market products for
genetic analysis based on a number of technologies and are developing additional
DNA probe-based products. Many of these companies have substantially greater
capital resources, larger research and development and marketing staffs and
facilities and greater experience in developing products than we have.
Furthermore, our specific field in which we operate is subject to significant
and rapid technological change. Accordingly, even if we successfully introduce
our products or proposed products, we risk that our technologies will be
replaced by new technologies or that our products or proposed products will be
obsolete or non-competitive.

Dependence on Key Personnel

        We are dependent upon our key management and technical personnel and
consultants, and our future success will depend in part upon our ability to
retain these persons and to recruit additional qualified personnel. We must
compete with other companies, universities, research entities and other
organizations in order to attract and retain highly qualified personnel.
Although we have entered into agreements with our key executive officers, we
make no guarantee that we will retain such highly qualified personnel or hire
additional qualified personnel. We currently maintain no key man life insurance
on any of our management or technical personnel.

No Dividends Paid and None Anticipated

        We have never paid dividends on our common stock and do not plan to in
the foreseeable future, as any earnings will be invested in the further
expansion of our business.


                                       11


<PAGE>   12

Volatility of Stock Price

        The market price of our common stock may fluctuate significantly. We are
in the biotechnology industry and the market price of securities of
biotechnology companies have fluctuated significantly and these fluctuations
have often been unrelated to the companies' operating performance. Announcements
by us or our competitors concerning technological innovations, new products,
proposed governmental regulations or actions, developments or disputes relating
to patents or proprietary rights, and other factors that affect the market
generally could significantly impact our business and the market price of our
securities. Sales of our securities by existing security holders could also
significantly impact the market price of our securities.

Shares Eligible for Future Sale; Dilution

        Sales of substantial numbers of shares of our common stock in the public
market could substantially reduce the prevailing market price of our common
stock. As of March 31, 2000, 24,314,511 shares of our common stock were
outstanding; 2,020,590 shares of our common stock were issuable upon exercise
of outstanding warrants at exercise prices ranging from $0.50 to $2.50 per
share; and an additional 1,646,166 shares of our common stock were issuable upon
exercise of outstanding options at exercise prices ranging from $0.30 to $17.44
per share. Of the outstanding shares of common stock and shares issuable upon
exercise of warrants and options, substantially all are freely tradable by the
holders of such securities without restriction. If these holders sell a large
number of shares of our common stock in the public market, such sales could
substantially reduce the prevailing market price of our common stock. To the
extent the trading price of our common stock exceeds the exercise price of
options or warrants at the time such options or warrants are exercised, such
exercise will have a dilutive effect on the other stockholders.


                                       12

<PAGE>   13

                           PART II. OTHER INFORMATION

ITEM 1. LEGAL PROCEEDINGS

        Epoch is not a party to any material legal proceedings.

ITEM 6. EXHIBITS AND REPORTS ON FORM 8K

        (a) EXHIBITS

            27.1 -- Financial Data Schedule

        (b) REPORTS ON FORM 8K

            None


                                       13

<PAGE>   14

                                   SIGNATURES

        In accordance with the requirements of the Exchange Act, the registrant
caused this report to be signed on its behalf by the undersigned, thereunto duly
authorized.


                                           Epoch Pharmaceuticals, Inc.


Date: May 15, 2000                         By: /s/ Sanford S. Zweifach
                                           -------------------------------------
                                               Sanford S. Zweifach
                                               President/Chief Financial Officer


                                       14
<PAGE>   15
                                 EXHIBIT INDEX

               EXHIBIT
               NUMBER             DESCRIPTION
               -------            -----------

                27.1         Financial Data Schedule