<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 OF THE SECURITIES
         EXCHANGE ACT OF 1934 FOR THE QUARTERLY PERIOD ENDED JUNE 30, 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)

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

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

                                 (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 August 8, 2000
                   -----                   -----------------------------

        Common Stock, $.01 par value                 24,859,619


                               Page 1 of 14 Pages

<PAGE>   2

                           EPOCH PHARMACEUTICALS, INC.
                              INDEX TO FORM 10-QSB

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

     Item 1.  Financial Statements

              Balance Sheets as of December 31, 1999
              and June 30, 2000 (unaudited)...................................    3

              Statements of Operations (unaudited) for the three and six
              months ended June 30, 1999 and 2000.............................    4

              Statements of Cash Flows (unaudited) for the six months ended
              June 30, 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>
                                                                                    JUNE 30,
                                                                DECEMBER 31,          2000
                                                                   1999            (UNAUDITED)
                                                                ------------       ------------
<S>                                                             <C>                <C>
Current assets:
    Cash and cash equivalents ............................      $  1,772,274       $ 18,036,078
    Receivables ..........................................            20,073             41,452
    Prepaid expenses .....................................            34,188            161,195
                                                                ------------       ------------
       Total current assets ..............................         1,826,535         18,238,725

Equipment, net ...........................................           399,705            691,784

Restricted cash ..........................................                --            606,926
License rights ...........................................                --            553,194
Other assets .............................................            39,344             36,419
                                                                ------------       ------------

       Total assets ......................................      $  2,265,584       $ 20,127,048
                                                                ============       ============

                           LIABILITIES AND STOCKHOLDERS' EQUITY
Current liabilities:
    Accounts payable .....................................      $    102,884       $    223,826
    Accrued liabilities ..................................           393,660            493,906
    Deferred revenue - current portion ...................           277,742            277,742
                                                                ------------       ------------
       Total current liabilities .........................           774,286            995,474

Deferred revenue .........................................         1,316,129          1,289,758

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 24,859,619 at June 30, 2000 .           193,824            248,596
    Additional paid-in capital ...........................        61,625,990         81,581,221
    Deferred stock compensation ..........................          (111,874)           (87,898)
    Accumulated deficit ..................................       (61,532,771)       (63,900,103)
                                                                ------------       ------------

       Total stockholders' equity ........................           175,169         17,841,816
                                                                ------------       ------------

Commitments and subsequent events

Total liabilities and stockholders' equity ...............      $  2,265,584       $ 20,127,048
                                                                ============       ============
</TABLE>


                 See accompanying notes to financial statements.


                                       3
<PAGE>   4

                           EPOCH PHARMACEUTICALS, INC.
                            STATEMENTS OF OPERATIONS
                                   (UNAUDITED)

<TABLE>
<CAPTION>
                                                           THREE MONTHS ENDED                    SIX MONTHS ENDED
                                                                 JUNE 30,                             JUNE 30,
                                                     -------------------------------       -------------------------------
                                                         1999               2000               1999               2000
                                                     ------------       ------------       ------------       ------------
<S>                                                  <C>                <C>                <C>                <C>
Revenue:
  Product sales ...............................      $         --       $    127,520       $         --       $    212,720
  License fees ................................                --             13,184                 --             26,370
  Research contract revenue ...................            57,525                 --            152,617                 --
                                                     ------------       ------------       ------------       ------------
     Total revenue ............................            57,525            140,704            152,617            239,090

Operating expenses:
  Research and development ....................           653,215            744,236          1,297,816          1,477,976
  General and administrative ..................           318,770            812,039            653,635          1,529,269
                                                     ------------       ------------       ------------       ------------
     Total operating expenses .................           971,985          1,556,275          1,951,451          3,007,245
                                                     ------------       ------------       ------------       ------------

     Operating loss ...........................          (914,460)        (1,415,571)        (1,798,834)        (2,768,155)

Other income (expense):
  Interest income .............................            13,374            274,629             31,927            400,976
  Interest and financing expense ..............          (233,039)                --           (463,604)              (153)
                                                     ------------       ------------       ------------       ------------
     Loss from continuing operations ..........        (1,134,125)        (1,140,942)        (2,230,511)        (2,367,332)

Discontinued operations -
 gain on disposal of discontinued operations ..            30,000                 --             70,000                 --
                                                     ------------       ------------       ------------       ------------

     Net loss .................................      $ (1,104,125)      $ (1,140,942)      $ (2,160,511)      $ (2,367,332)
                                                     ============       ============       ============       ============

Loss per share from continuing operations -
 basic and diluted ............................      $      (0.08)      $      (0.05)      $      (0.15)      $      (0.10)
Income per share from discontinued operations -
 basic and diluted ............................                --                 --                 --                 --
                                                     ------------       ------------       ------------       ------------

Net loss per share - basic and diluted ........      $      (0.08)      $      (0.05)      $      (0.15)      $      (0.10)
                                                     ============       ============       ============       ============

Weighted average number of common shares
 outstanding - basic and diluted ..............        14,872,838         24,786,698         14,851,762         23,152,798
</TABLE>


                 See accompanying notes to financial statements.


                                       4
<PAGE>   5

                           EPOCH PHARMACEUTICALS, INC.
                            STATEMENTS OF CASH FLOWS
                                   (UNAUDITED)

<TABLE>
<CAPTION>
                                                                                    SIX MONTHS ENDED
                                                                                        JUNE 30,
                                                                             ------------------------------
                                                                                1999               2000
                                                                             -----------       ------------
<S>                                                                          <C>               <C>
Cash flows from operating activities:
    Net loss ..........................................................      $(2,160,511)      $ (2,367,332)

    Adjustments to reconcile net loss to net cash provided by (used in)
        operating activities:
       Depreciation and amortization ..................................           44,984             75,578
       Amortization of deferred financing expense .....................          333,342                 --
       Amortization of deferred stock compensation ....................           23,976             23,976
       Stock compensation charge ......................................               --             94,400
       Amortization of license rights .................................               --              3,057
       Changes in operating assets and liabilities:
          Receivables .................................................          (64,324)           (21,379)
          Prepaid expenses and other assets ...........................           22,619           (124,081)
          Accounts payable ............................................          (24,538)           120,942
          Accrued interest on note payable to related party ...........          129,409                 --
          Accrued expenses for canceled relocation ....................         (287,397)                --
          Deferred revenue ............................................        2,300,000            (26,371)
          Other accrued liabilities ...................................          (12,640)           100,246
                                                                             -----------       ------------
              Net cash provided by (used in) operating activities .....          304,920         (2,120,964)
                                                                             -----------       ------------

Cash flows from investing activities:
    Security deposit on new facilities ................................               --           (606,926)
    Investment in license rights ......................................               --           (250,000)
    Investment in leasehold improvements on new facilities ............               --           (158,634)
    Acquisition of equipment ..........................................         (211,647)          (209,023)
                                                                             -----------       ------------
       Net cash used in investing activities ..........................         (211,647)        (1,224,583)

Cash flows from financing activities:
    Proceeds from sale of common stock ................................               --         10,000,039
    Proceeds from exercise of warrants ................................               --          9,551,280
    Proceeds from exercise of stock options ...........................           53,837             58,032
                                                                             -----------       ------------
       Net cash provided by financing activities ......................           53,837         19,609,351
                                                                             -----------       ------------

Net increase in cash and cash equivalents .............................          147,110         16,263,804
Cash and cash equivalents at beginning of period ......................          658,363          1,772,274
                                                                             -----------       ------------
Cash and cash equivalents at end of period ............................      $   805,473       $ 18,036,078
                                                                             ===========       ============

Supplemental disclosure of cash flow information - issuance of common
    stock in exchange for license rights ..............................      $        --       $    306,250
                                                                             ===========       ============
Supplemental disclosure of cash flow information -
    cash payments made during the period for interest .................      $       852       $        157
                                                                             ===========       ============
</TABLE>


                 See accompanying notes to financial statements.


                                       5
<PAGE>   6

                           EPOCH PHARMACEUTICALS, INC.
                          NOTES TO FINANCIAL STATEMENTS
                                  JUNE 30, 2000
                                   (UNAUDITED)

NOTE (1) 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 (2) 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 (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 June 30, 2000, there were 1,693,250 options outstanding to
purchase the common stock of Epoch with exercise prices ranging from $0.30 to
$14.63. Also outstanding at June 30, 2000 were 1,549,348 warrants to purchase
the common stock of Epoch with exercise prices ranging from $0.50 to $16.00 per
share. At


                                       6
<PAGE>   7

June 30, 1999, there were 1,398,624 options outstanding to purchase the common
stock of Epoch with exercise prices ranging from $0.30 to $5.88. Also
outstanding at June 30, 1999 were 7,798,875 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)  LICENSE AGREEMENT

         In June 2000, we licensed from Louisiana State University, LSU, the
rights to use certain technologies covered by a U. S. Patent held by LSU. We
paid $250,000 in cash and issued 50,000 shares of our common stock, valued at
$306,250, in return for the license. The license rights are being amortized on
the straight-line method over the life of the patent, which expires in 2015.

NOTE (6)  STOCKHOLDERS' EQUITY

         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 3,798,762 shares of common stock were
exercised generating $9,497,000 in cash. In addition to the warrant call, the
exercise of other miscellaneous warrants generated $54,000.

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


                                       7
<PAGE>   8

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".

                              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 represent 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 represents revenue
from U.S. government grants and contracts, and subcontracts. The company had no
active grants in the first six months of 2000.

         Research and Development. Research and development expenses increased
$91,000 for the quarter and $180,000 for the six months ended June 30, 2000,
respectively, in relation to comparable 1999 periods. The increases in the
current year expenses are primarily the result of:

         o  Epoch's subcontracting support work on research and development to
            an outside firm in 2000 in the amount of $67,000 of which $11,000
            was expended in the second quarter. The short-term contract was
            concluded in May 2000.

         o  Increased travel expense of $45,000 during the first six months of
            the year as our scientists have been presenting our technologies to
            other companies and the scientific community as we increase our
            efforts to commercialize our products, with $27,000 of this increase
            incurred during the second quarter of 2000.

         o  Increased depreciation expense of $27,000 for the year, or $12,000
            for the quarter. The Company has acquired additional capital
            equipment with a portion of the funding received in 2000.

         o  Additional variations in research and development expense are the
            result of normal business fluctuations.

         General and Administrative. General and administrative expenses
increased $493,000 in the quarter and $876,000 in the six months ended June 30,
2000 compared to the respective prior year periods. The increase in 2000 periods
is primarily the result of:


                                       8
<PAGE>   9

         o  $150,000 in expenses incurred in connection with a warrant call and
            private placement completed during the six month period ended June
            30, 2000.

         o  Fees paid to The Nasdaq National Market in the amount of $94,000 in
            the second quarter of 2000.

         o  An increase in expenses for investor relations services of $132,000
            for the six month period, or $116,000 for the quarter ended June 30,
            2000. We issued a three year warrant for a total of 25,000 shares of
            common stock at exercise prices ranging from $8.00 to $16.00. We
            recognized $94,000 in expense in conjunction with issuing this
            warrant.

         o  An increase of $64,000 in expenditures associated with the filing of
            patents over the prior six month period. In the first six months of
            2000, we incurred $111,000 in fees toward filing patents on new
            technologies, as compared to $47,000 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 $137,000 in compensation related to
            additional executive personnel, of which $75,000 is pertinent to the
            second quarter.

         o  Expenditures of $72,000 for the six month period and for the quarter
            ended June 30, 2000, on executive searches for open management
            positions.

         o  A rent increase of $41,000 for the six month period, or $19,000 for
            the quarter ended June 30, 2000.

         o  Increased travel expense of $49,000 for the six month period, or
            $28,000 for the quarter ended June 30, 2000.

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

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

         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. No payments have been received in 2000.


                                       9
<PAGE>   10

                         LIQUIDITY AND CAPITAL RESOURCES

         At June 30, 2000 we had operating cash and cash equivalents of
$18,036,000. 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.

         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 3,798,762 shares of common stock were
exercised generating $9,497,000 in cash. In addition to the warrant call, the
exercise of other miscellaneous warrants generated $54,000.

         Management estimates that the June 30, 2000 cash balance 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.

         In February 2000 we entered into a 12-year non-cancelable lease for a
25,000 square foot facility in Bothell, Washington. We began construction of the
tenant improvements in June 2000. We anticipate an investment of approximately
$3,719,000 for the design and construction of tenant improvements, which are
scheduled for completion in November 2000. These cash outlays will be partially
offset by payments from the landlord of approximately $1,500,000.

         Cash increased by $16,264,000 during the period primarily as a result
of the net of $10,000,000 received from the private placement and $9,551,000
from the exercise of warrants offset by normal expenditures on operations, the
acquisition of $209,000 of capital equipment, $159,000 invested in the new
facility, $607,000 security deposit on the new facility, and the cash payment of
$250,000 to LSU for the patent license. The comparable period of the prior year
had a cash increase of $147,000, the net result of $2,300,000 received from the
PE Biosystems license agreement offset by normal operating expenditures and the
acquisition of $212,000 of equipment used in research and development.

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

                          NEW ACCOUNTING PRONOUNCEMENTS

         In June 2000 the SEC issued Staff Accounting Bulletin No. 101B. SAB
101B delays the effective date of Staff Accounting Bulletin No. 101, "Revenue
Recognition in Financial Statements," to the fourth quarter for fiscal years
beginning December 15, 1999. SAB 101 provides guidance on revenue recognition
and the SEC staff's views on the application of accounting principles to
selected revenue recognition issues. The interpretation of SAB 101 is currently
uncertain as it relates to biotechnology


                                       10
<PAGE>   11

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

We have never been profitable and anticipate future losses

         We have never been profitable. Since our formation in 1985, we have
generated limited revenues. As of June 30, 2000, we had an accumulated deficit
of approximately $64 million. We expect to incur additional losses as we expand
our research and development efforts. We will need additional funds to continue
our research and development activities.

There is a risk that our technology may not be effective or might not work

         The science and technology of synthetic DNA-based products is rapidly
evolving. Our proposed products are in the discovery or early development stage.
The proposed products will require significant further research, development,
and testing. We face the risk that any or all of our proposed products could
prove to be ineffective or unsafe, or be an inferior product to products
marketed by others because our products are based on new and unproven innovative
technologies. We cannot predict whether our research and development activities
will result in any commercially viable products. If we do not have commercially
viable products, we will not be able to generate funds internally to support
operations.

There is a risk that we do not own exclusive rights to our technology and our
competition may have access to our technology which may prevent us from selling
our products

         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. Further, third parties may hold proprietary rights,
which precede our claims and, therefore, could prohibit us from marketing the
proposed products.

Some of our technology might infringe on the rights of others, which may prevent
us from selling our products

         There is a great deal of litigation regarding patents and other
intellectual property rights in the biomedical industry. We were defendants in
one action of this kind which we settled prior to 1997. Although patent and
intellectual property disputes in the biomedical area are sometimes settled
through licensing or similar arrangements, this kind of solution can be
expensive, if a license can be obtained at


                                       11
<PAGE>   12

all. 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 business.

We face numerous competitors and changing technologies which could make our
products obsolete

         Many companies do research and development and market products designed
to diagnose conditions based on a number of technologies and are developing
additional products using gene-based technologies. 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. Even if we successfully introduce
our products or proposed products, our technologies could be replaced by new
technologies or our products or proposed products might be obsolete or
non-competitive.

The loss of key personnel could adversely affect operations by impairing our
research and our efforts to commercialize and license our products

         Our performance is greatly dependent upon our key management including
our CEO, Dr. Gerber, and technical personnel and consultants. Our future success
will depend in part upon our ability to retain these people 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 these
highly qualified personnel or hire additional qualified personnel. We currently
maintain no key man life insurance on any of our management or technical
personnel.

The value of our common stock could change significantly in a very short time

         The market price of our common stock may fluctuate significantly. For
example, in the first quarter of 2000, our stock traded as high as $25.00 and as
low as $2.87. The rapid price changes Epoch has experienced recently, and
throughout our history, place your investment in our common stock at risk of
total loss over a short period of time. 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.

The price of our common stock could decrease because more shares will be fully
tradable

         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 June 30, 2000, 24,859,619 shares of our common stock were
outstanding; 1,549,348 shares of our common stock were issuable upon exercise of
outstanding warrants at exercise prices ranging from $0.50 to$16.00 per share;
and an additional 1,693,250 shares of our common stock were issuable upon
exercise of outstanding options at exercise prices ranging from $0.30 to $14.63
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 these securities without restriction. If these holders sell a large
number of shares of our common stock in the public market, these 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 the options or warrants are exercised, the
exercise will have a dilutive effect on the other stockholders.


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<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

                  On May 8, 2000 a report on Form 8K was filed reporting that
                  Epoch had been approved for listing on The Nasdaq National
                  Market.


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<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:  August 14, 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