EPOCH BIOSCIENCES INC
POS AM, 2000-12-28
IN VITRO & IN VIVO DIAGNOSTIC SUBSTANCES
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<PAGE>   1

   As filed with the Securities and Exchange Commission on December 28, 2000
                                                      Registration No. 333-88909

                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549

                         POST-EFFECTIVE AMENDMENT NO. 1
                                   ON FORM S-3
                                       TO
                                    FORM SB-2
                             REGISTRATION STATEMENT
                                      Under
                           The Securities Act of 1933

                             EPOCH BIOSCIENCES, INC.
                       (NAME OF REGISTRANT IN ITS CHARTER)
<TABLE>
<S>                                   <C>                                        <C>
       DELAWARE                                   2834                                 91-1311592
(STATE OR OTHER JURISDICTION          (PRIMARY STANDARD INDUSTRIAL                  (I.R.S. EMPLOYER
OF INCORPORATION OR ORGANIZATION)             CODE NUMBER)                       IDENTIFICATION NUMBER)
</TABLE>

       21720 23rd Drive, S.E., N.E., Suite 150, Bothell, Washington 98021
                                 (425) 482-5555
          (ADDRESS AND TELEPHONE NUMBER OF PRINCIPAL EXECUTIVE OFFICES)

       21720 23rd Drive, S.E., N.E., Suite 150, Bothell, Washington 98021
                                 (425) 482-5555
                    (ADDRESS OF PRINCIPAL PLACE OF BUSINESS)

                William G. Gerber, M.D., Chief Executive Officer
       21720 23rd Drive, S.E., N.E., Suite 150, Bothell, Washington 98021
                                 (425) 482-5555
           (NAME, ADDRESS AND TELEPHONE NUMBER OF AGENT FOR SERVICE)

                                   COPIES TO:
                             C. CRAIG CARLSON, ESQ.
                             LAWRENCE B. COHN, ESQ.
                         STRADLING YOCCA CARLSON & RAUTH
                      660 NEWPORT CENTER DRIVE, SUITE 1600
                         NEWPORT BEACH, CALIFORNIA 92660
                                 (949) 725-4000

        APPROXIMATE DATE OF COMMENCEMENT OF PROPOSED SALE TO THE PUBLIC:
     From time to time after this Registration Statement becomes effective.

   If this Form is filed to register additional securities for an offering
pursuant to Rule 462(b) under the Securities Act of 1933, please check the
following box and list the Securities Act registration statement number of the
earlier effective registration statement for the same offering. [ ]

   If this Form is a post-effective amendment filed pursuant to Rule 462(c)
under the Securities Act, check the following box and list the Securities Act
registration statement number of the earlier effective registration statement
for the same offering. [ ]

   If this Form is a post-effective amendment filed pursuant to Rule 462(d)
under the Securities Act, check the following box and list the Securities Act
registration statement number of the earlier effective registration statement
for the same offering. [ ]

   If delivery of the prospectus is expected to be made pursuant to Rule 434,
please check the following box. [ ]

   If any of the securities being registered on this Form are to be offered on a
delayed or continuous basis pursuant to Rule 415 under the Securities Act, check
the following box: [X]

<TABLE>
<CAPTION>
---------------------------------------------------------------------------------------------------------
                                    CALCULATION OF REGISTRATION FEE
---------------------------------------------------------------------------------------------------------
    TITLE OF EACH CLASS OF         PROPOSED MAXIMUM     PROPOSED MAXIMUM   AGGREGATE        AMOUNT OF
          SECURITIES                 AMOUNT TO BE          AGGREGATE       OFFERING        REGISTRATION
       TO BE REGISTERED             REGISTERED(1)      OFFERING PRICE(2)    PRICE             FEE(3)
=========================================================================================================
<S>                                <C>                 <C>                 <C>             <C>
 Common stock, par value: $.01      100,000 shares          $5.00          $500,000           $125.00
           per share
=========================================================================================================
</TABLE>

(1)     Epoch originally registered for resale by security holders 10,428,365
        shares of common stock under Registration No. 333-12601 on Form SB-2 and
        1,268,258 shares of common stock under Registration No. 333-21353 on
        Form SB-2. Pursuant to Rule 429, the prospectus included as part of this
        Registration Statement also relates to the resale of these previously
        registered shares. Epoch has previously paid registration fees of
        $3,796.47 with respect to these shares. Additionally, Epoch previously
        paid registration fees totaling $14,099.52 to register 7,089,560 shares
        of common stock under this Registration Statement.

(2)     The offering price is estimated solely for the purpose of calculating
        the registration fee in accordance with Rule 457(C), using the average
        of the high and low price reported by The Nasdaq National Market for the
        common stock on December 27, 2000, which was approximately $5.00 per
        share.

(3)     We previously paid registration fees of $1,660.52 for the registration
        of 3,472,738 shares of common stock when this Registration Statement was
        initially filed on October 13, 1999, $12,278 in connection with the
        registration of an additional 3,566,822 shares of common stock upon the
        filing of Amendment No. 1, and $161 in connection with the registration
        of an additional 50,000 shares of common stock upon the filing of
        Amendment No. 2.

        The Registrant hereby amends this registration statement on such date or
dates as may be necessary to delay its effective date until the Registrant shall
file a further amendment which specifically states that this Registration
Statement shall thereafter become effective in accordance with Section 8(a) of
the Securities Act of 1933 or until the Registration Statement shall become
effective on such date as the Securities and Exchange Commission, acting
pursuant to said Section 8(a) may determine.



<PAGE>   2

PROSPECTUS

                             EPOCH BIOSCIENCES, INC.

                             Shares of Common Stock


        The stockholders listed in this prospectus under the section entitled
"Selling Stockholders" may offer and sell a total of 10,508,916 shares of common
stock, which they own or have the right to acquire from time to time. The shares
of common stock included in this offering include 1,386,184 shares issuable upon
the exercise of warrants.

                               ------------------

        Our common stock is currently traded on The Nasdaq National Market under
the symbol "EBIO".

                               ------------------

        INVESTING IN THE COMMON STOCK INVOLVES A HIGH DEGREE OF RISK. SEE THE
SECTION TITLED "RISK FACTORS" BEGINNING ON PAGE 2 OF THIS PROSPECTUS.

                               ------------------

        Neither The Securities and Exchange Commission nor any state securities
commission has approved or disapproved of these securities, or determined if
this prospectus is truthful or complete. Any representation to the contrary is a
criminal offense.

                               ------------------

                The date of this prospectus is December 28, 2000.



<PAGE>   3

                                TABLE OF CONTENTS
<TABLE>
<CAPTION>
                                                                                          PAGE
                                                                                          ----
<S>                                                                                       <C>
Prospectus Summary...........................................................................1
Risk Factors.................................................................................2
Year 2000 Compliance.........................................................................4
Forward Looking Statements...................................................................4
Selling Stockholders.........................................................................5
Plan of Distribution.........................................................................8
Use of Proceeds..............................................................................8
Legal Matters................................................................................8
Experts......................................................................................8
Where You Can Find Additional Information....................................................8
Incorporation of Certain Documents by Reference..............................................9
Part II -- Information Not Required in Prospectus.........................................II-1
Signatures................................................................................II-4
Exhibit Index.............................................................................II-6
</TABLE>



<PAGE>   4

                               PROSPECTUS SUMMARY

        This summary highlights information, including the financial statements
and related notes incorporated by reference in this prospectus and this summary,
may exclude information that you should consider before investing in the common
stock offered in this prospectus. You should read the entire prospectus
carefully.

        The number of shares outstanding as of December 21, 2000, is 25,010,784.
This number does not include 1,897,843 shares reserved for issuance upon the
exercise of outstanding stock options, or 1,386,184 shares reserved for issuance
upon the exercise of outstanding warrants.

        We will not receive any proceeds from the selling stockholders' sale of
the shares of common stock covered by this prospectus. However, some of the
common stock which may be sold under this prospectus will require the selling
stockholder to first exercise warrants. We would receive the proceeds from the
exercise of any warrants, which we would use to fund our research and
development activities and for general corporate purposes.

BUSINESS OF EPOCH BIOSCIENCES, INC.

        Epoch Biosciences, Inc. develops and intends to commercialize unique,
proprietary technologies to enhance the study of genes in plants, animals and
humans. Our technology is based on our expertise in DNA chemistry, which allows
us to design, synthesize and modify oligonucleotides, or synthetic strands of
DNA, that more selectively bind to and interact with their target genes, or the
gene of interest. Our technology has broad application potential in the
developing fields of molecular diagnostics and the study of genes, including the
detection of infectious diseases, inheritable diseases through prenatal testing,
screening populations to identify landmarks on the gene which correlate with
disease risk or drug response, as well as any other genetic analysis based on
DNA sequence determination.

        We incorporated in Delaware on August 14, 1985, under the name
MicroProbe Corporation. We changed our name to Epoch Pharmaceuticals, Inc. in
December 1995. We further changed our name to Epoch Biosciences, Inc. in August
2000. Our principal office is located at 21720 23rd Drive, S.E., N.E., Suite
150, Bothell, Washington 98021, and our telephone number is (425) 482-5555.



                                       1
<PAGE>   5

                                  RISK FACTORS

        Investing in the common stock offered by the selling stockholders is
very risky. You should be able to bear a complete loss of your investment. You
should carefully consider the following factors and other information in this
prospectus before deciding to invest in shares of our common stock offered by
the selling stockholders.

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 September 30, 2000, we had an accumulated
deficit of approximately $65 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. Some of our current research and development activities may not
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.

We have limited manufacturing experience

        While Epoch has experience in researching and developing unique,
proprietary technologies to enhance the study of genes, our experience in
manufacturing our products is relatively limited. While we are beginning to
produce and supply products to customers for commercial use, we do not currently
have the capacity for high-volume production. We will need to expand our
manufacturing capacity in connection with our continued development and
commercialization of our products. Any delay or inability to expand our
manufacturing capacity could materially adversely affect our manufacturing
ability.

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



                                       2
<PAGE>   6

        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 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 December 21, 2000, 25,010,784 shares of our common stock were outstanding;
1,386,184 shares of our common stock were



                                       3
<PAGE>   7

issuable upon exercise of outstanding warrants at exercise prices ranging from
$0.50 to$16.00 per share; and an additional 1,897,843 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.

                           FORWARD LOOKING STATEMENTS

        Some of the information included in this prospectus contains
forward-looking statements. These statements can be identified by the use of
forward-looking terms like "may," "will," "expect," "anticipates," "estimate,"
"continue," or other similar words. These statements discuss future
expectations, projections or results of operations or of financial condition or
state other "forward-looking" information. When considering these
forward-looking statements, you should keep in mind the risk factors and other
cautionary statements we make. These risk factors could cause our actual results
to differ materially from those contained in any forward-looking statement. If
any of the above risks actually occur, our business could be harmed and the
trading price of our common stock could decline.



                                       4
<PAGE>   8

                              SELLING STOCKHOLDERS

<TABLE>
<CAPTION>
                                                   SHARES OWNED
                                                  BEFORE OFFERING                              AMOUNT AND
                                                   (INCLUDING                               PERCENTAGE OF
                                                  SHARES ISSUABLE      SHARES OFFERED            SHARES
                                                  UPON EXERCISE OF    PURSUANT TO THIS      BENEFICIALLY OWNED
SELLING STOCKHOLDER                                   WARRANTS)        PROSPECTUS(1)          AFTER OFFERING
-------------------                               ----------------    ----------------      ------------------
<S>                                               <C>                 <C>                   <C>
American Masters Fund, "Hilspen Series" ........         53,200           53,200                     0
Amerindo Investment Advisors, Inc. .............        285,715          285,715                     0
The Alfred J. Anzalone Family Ltd.
  Partnership ..................................         40,000           40,000                     0
Michael Arnouse ................................         30,000           30,000                     0
Batterson, Johnson & Wang Limited
  Partners .....................................        258,145          258,145                     0
Bay City Capital(2) ............................      2,920,000        2,920,000                     0
Lamon Lynn Bennett .............................         73,000           73,000                     0
Harbor Trust ...................................        500,000          500,000                     0
Burrill & Craves(3) ............................         83,334           83,334                     0
James F. Clark .................................         25,000           25,000                     0
James L. Comazzi ...............................         10,500           10,500                     0
Concept Mining, Inc. ...........................         44,000           44,000                     0
Cooley, Godward ................................         25,000           25,000                     0
John S. Dehne & Carol A. Dehne .................         37,500           12,500                25,000*
Donaldson, Lufkin, Jenrette
  Securities Corporation .......................         13,000           13,000                     0
Fred B. Craves(4) ..............................        454,907          327,407               127,500*
First Security Van Kasper ......................         25,000           25,000                     0
Frontier Charitable Remainder, Nicolas
  Madonia (Trustee) ............................        140,000          140,000                     0
Corinna Funari .................................         12,500           12,500                     0
The Gerbsman Family Trust, DTD
  12-4-90, Steven R. or Marlene
  Gerbsman, Trustees ...........................         36,000           11,000                25,000*
Carl S. Goldfischer, M.D .......................          8,743            7,143                 1,600*
Goldman Sachs Performance Partners
  (Offshore), L.P. .............................         19,700           19,700                     0
Goldman Sachs Performance Partners, L.P ........         27,800           27,800                     0
Grace Brothers Ltd. ............................      5,249,693        2,200,000             3,049,693 (12.3%)
John P. Green, Jr ..............................         25,000           25,000                     0
Gsam Oracle Investments, Inc. FAO
  Mark Callow Gam Fund Management Limited.......         47,143           47,143                     0
Helen Gurman ...................................         25,000           25,000                     0
Jason C. Hackett ...............................          7,500            7,500                     0
Seth Harrison ..................................          7,143            7,143                     0
Joel Hedgpeth ..................................        350,000          350,000                     0
Louisa Heyward .................................         37,500           12,500                25,000*
Hilspen Capital Partners .......................         40,200           40,200                     0
Hilspen Capital Partners II ....................        159,800          159,800                     0
Hilspen Capital Partners I, L.P. ...............         19,200           19,200                     0
Hilspen Capital Partners II, L.P. ..............        165,815          165,815                     0
Billy B. & Lorraine S. Huff ....................         37,500           12,500                25,000*
Gerald Korman ..................................          8,500            8,500                     0
Paula Kramer ...................................         12,500           12,500                     0
Lone Cypress, Ltd. .............................        234,000          234,000                     0
</TABLE>



                                       5
<PAGE>   9

<TABLE>
<CAPTION>
                                                   SHARES OWNED
                                                  BEFORE OFFERING                              AMOUNT AND
                                                   (INCLUDING                               PERCENTAGE OF
                                                  SHARES ISSUABLE      SHARES OFFERED            SHARES
                                                  UPON EXERCISE OF    PURSUANT TO THIS      BENEFICIALLY OWNED
SELLING STOCKHOLDER                                   WARRANTS)        PROSPECTUS(1)          AFTER OFFERING
-------------------                               ----------------    ----------------      ------------------
<S>                                               <C>                 <C>                   <C>
Lone Sequoia, L.P. .............................         18,857           18,857                     0
Lone Balsam, L.P. ..............................         22,572           22,572                     0
Lone Spruce, L.P. ..............................         10,286           10,286                     0
Louisiana State University .....................         50,000           50,000                     0
The Low Family Trust, U/T/A 3-21-82
  Thomas B. Low, Trustee .......................         42,100           37,500                 4,600*
Mark D. Matteucci ..............................         10,000           10,000                     0
Joseph D. McKeown ..............................         37,500           12,500                25,000*
Kenneth L. Melmon ..............................         80,999           55,999                25,000*
Merlin Biomed International ....................         71,429           71,429                     0
Eric Miller ....................................         12,500           12,500                     0
MMC/GATX .......................................            100              100                     0
Narragansett I, L.P. ...........................         52,143           52,143                     0
Narragansett Offshore, Ltd. ....................         19,286           19,286                     0
Tolof O. Nasby .................................          5,000            5,000                     0
The Olmsted Group, L.L.C .......................        145,700          122,500                23,200*
Oracle Partners, L.P. ..........................        179,715          179,715                     0
Oracle Institutional Partners, L.P. ............         49,714           49,714                     0
Oracle Offshore Limited ........................          9,143            9,143                     0
Roy C. Page ....................................         38,955           26,999                11,956*
PE Corporation .................................        800,000          800,000                     0
Pensco Pension Services f/b/o
  Lawrence A. Mitchell IRA .....................        109,858           42,858                67,000*
Pharmawealth ...................................         71,429           71,429                     0
Richard Pops ...................................          7,143            7,143                     0
The Ridge Land Company .........................         44,000           44,000                     0
David Mark Rozen ...............................        250,000           62,500               187,500*
Bruce D. Schlerling TTEE
  the estate of David Blech Debtor .............        109,355          109,355                     0
Stuart G. Stanley ..............................         15,000           12,500                 2,500*
Michael Steifman ...............................         12,500           12,500                     0
Stern & Co. ....................................         25,000           25,000                     0
Robert N. Swetnick .............................          5,000            5,000                     0
Ursula Vollenweider ............................          7,143            7,143                     0
Susan Jane Walker ..............................         18,500            7,500                11,000*
Robert M. Wydro ................................         55,000           50,000                 5,000*
Raymond Zabel, Jr ..............................         12,500           12,500                     0
Marlee Zweifach(5)(6) ..........................        101,250          101,250                     0
Sanford S. Zweifach(6) .........................        126,250          101,250                25,000*
</TABLE>


---------------------

*       Less than one percent

(1)     Includes up to 1,386,184 shares issuable upon the exercise of warrants.

(2)     Represents 2,920,000 shares held by Bay City Capital Fund I, L.P. Bay
        City Capital, LLC, the general partner of Bay City Capital Fund I, L.P.,
        is a merchant banking partnership formed by The Craves Group and The
        Pritzker Family business interest. Fred Craves, Ph.D., the chairman of
        Epoch, is the majority owner and controlling person of The Craves Group.
        By virtue of their status as members of Bay City Capital, LLC, each of
        The Craves Group and The Pritzker Family may be deemed the beneficial
        owner of all of the shares held of record by Bay City Fund I, L.P. (the
        "Bay City Shares"). By virtue of his status as the majority owner and



                                       6
<PAGE>   10

        controlling person of The Craves Group, Fred Craves may also be deemed a
        beneficial owner of the Bay City Shares. Each of The Craves Group, The
        Pritzker Family and Fred Craves disclaims beneficial ownership of any
        Bay City Shares except to the extent, if any, of their actual pecuniary
        interest in those shares.

(3)     Includes warrants to purchase 83,334 shares which are held by Burrill &
        Craves, of which Fred Craves is a general partner. Also includes
        2,880,000 shares which are held by Bay City Capital, LLC. See footnote
        (2). Fred Craves disclaims beneficial ownership of the Bay City Capital
        shares except to the extent of his pecuniary interest in Bay City
        Capital, LLC.

(4)     Fred Craves is the chairman of the board of directors of Epoch.

(5)     Marlee Zweifach is the former spouse of Sanford Zweifach.

(6)     Sanford Zweifach is Epoch's President and Chief Financial Officer.



                                       7
<PAGE>   11

                              PLAN OF DISTRIBUTION

        Each selling stockholder has informed us that he, she or it may sell
common stock from time to time in transactions on The Nasdaq National Market, in
negotiated transactions, or otherwise, or by a combination of these methods, at
fixed prices which may be changed, at market prices at the time of sale, at
prices related to market prices or at negotiated prices. The selling
stockholders or their successors in interest may effect these transactions by
selling the common stock to or through broker-dealers, who may receive
compensation in the form of discounts, concessions or commissions from the
selling stockholders or the purchasers of the common stock for whom the
broker-dealer may act as an agent or to whom they may sell the common stock as a
principal, or both. The compensation to a particular broker-dealer may be in
excess of customary commissions.

        The selling stockholders or their successors in interest and
broker-dealers who act in connection with the sale of the common stock may be
considered "underwriters" within the meaning of the Securities Act, and any
commissions received by the broker-dealers and profits on any resale of the
common stock as a principal may be considered underwriting discounts and
commissions under the Securities Act.

        We have agreed to bear the expenses in connection with the registration
and sale of the common stock offered by the selling stockholders (other than
selling commissions and the fees and expenses of counsel or other advisors to
the selling stockholders) which we estimate to be $67,225.

                                 USE OF PROCEEDS

        We will not receive any proceeds from the selling stockholders' sale of
the shares of common stock. However, some of the common stock which may be sold
under this prospectus will require the selling stockholder to first exercise
warrants. We would receive the proceeds from the exercise of any warrants, which
we would use to fund our research and development activities and for general
corporate purposes.

                                  LEGAL MATTERS

        The validity of the common stock offered in this prospectus will be
passed upon for us by Stradling Yocca Carlson & Rauth, a Professional
Corporation, Newport Beach, California.

                                     EXPERTS

         The financial statements of Epoch Biosciences, Inc. (formerly Epoch
Pharmaceuticals, Inc.) as of December 31, 1999 and for each of the years in the
two-year period ended December 31, 1999 have been incorporated by reference into
this prospectus and in this registration statement in reliance on the report of
KPMG LLP, independent certified public accountants, incorporated by reference
into this prospectus and upon the authority of said firm as experts in
accounting and auditing.

                       WHERE YOU CAN FIND MORE INFORMATION

        We are a "small business issuer" under the Securities Act. We are also
required by the Exchange Act to file annual, quarterly and special reports,
proxy statements and other information with the SEC. Our SEC filings are
available to the public over the Internet at the SEC's web site at
http://www.sec.gov. You



                                       8
<PAGE>   12

may also read and copy any document we file with the SEC at its public reference
facilities at 450 Fifth Street, N.W., Washington, D.C. 20549; 7 World Trade
Center, Suite 1300, New York, New York 10048; and Citicorp Center, 500 West
Madison Street, Suite 1400, Chicago, Illinois 60661-2511. You may also obtain
copies of the documents at prescribed rates by writing to the Public Reference
Section of the SEC at 450 Fifth Street, N.W., Washington, D.C. 20549. Please
call the SEC at 1-800-SEC-0330 for further information on the operation of the
public reference facilities.

        We originally registered for resale by the selling stockholders
10,428,365 shares of common stock under Registration No. 333-12601 and 1,268,258
shares of common stock under Registration No. 333-21353. Pursuant to Rule 429 of
the Securities Act, this prospectus relates to the resale of shares of common
stock covered by both registration statements. The registration statements
contain more information than this prospectus does about us and our securities.
We excluded parts which were not required by the SEC. To obtain further
information about us, please refer to the registration statements and their
exhibits, which you can inspect without charge by visiting the SEC's public
reference facilities listed in the prior paragraph. You can obtain copies of all
or any part of the registration statement and its exhibits by writing to the
SEC's Public Reference Section at Room 1024, 450 Fifth Street, N.W., Washington,
D.C. 20549 after payment of the fees prescribed by the SEC. You should rely only
on the information contained in this prospectus or any supplement. We have not
authorized anyone else to provide you with different information. You should not
assume that the information in this prospectus or any supplement or in the
documents incorporated by reference is accurate on any date other than the date
on the front of those documents.

                       DOCUMENTS INCORPORATED BY REFERENCE

        The SEC allows us to "incorporate by reference" the information we file
with the SEC, which means that we can disclose important information to you by
referring to those documents. We incorporate by reference the documents listed
below and any additional documents filed by us with the SEC under Section 13(a),
13(c), 14 or 15(d) of the Securities Exchange Act of 1934 until this offering of
securities is terminated. The information we incorporate by reference is an
important part of this prospectus, and any information that we file later with
the SEC will automatically update and supersede this information.

        The documents we incorporate by reference are:

                1. our Annual Report on Form 10-KSB for the fiscal year ended
        December 31, 1999;

                2. our Quarterly Report on Form 10-QSB for the fiscal quarter
        ended March 31, 2000;

                3. our Quarterly Report on Form 10-QSB for the fiscal quarter
        ended June 30, 2000;

                4. our Quarterly Report on Form 10-QSB for the fiscal quarter
        ended September 30, 2000;

                5. our Current Report on Form 8-K, dated May 8, 2000;

                6. our Current Report on Form 8-K, dated August 25, 2000;

                7. our Current Report on Form 8-K, dated November 27, 2000;

                8. our Preliminary Proxy Statement on Schedule 14A filed with
        the SEC on July 7, 2000;



                                       9
<PAGE>   13

                9. our Definitive Proxy Statement on Schedule 14A filed with the
        SEC on July 18, 2000;

                10. the description of our capital stock contained in our
        Registration Statement on Form 8-A12G, filed on July 30, 1993, including
        any amendment or report filed for the purpose of updating such
        description; and

                11. all other reports filed by us pursuant to Section 13(a), 14
        or 15(d) of the SEC Exchange Act since December 31, 1999.

        Any statement contained in a document incorporated or deemed to be
incorporated by reference herein shall be deemed to be modified or superseded
for purposes of this prospectus to the extent that a statement contained herein,
or in any other subsequently filed document that also is or is deemed to be
incorporated by reference herein, modifies or supersedes such statement. Any
statement so modified or superseded shall not be deemed, except as so modified
or superseded, to constitute a part of this prospectus.

        You may request a copy of these filings, at no cost, by writing or
calling us at Epoch Biosciences, 21720 23rd Drive, S.E., N.E., Suite 150,
Bothell, Washington 98021, telephone number (425) 482-5555, Attention: Larry J.
Larson.

        You should rely only on the information contained in this prospectus or
any supplement and in the documents incorporated by reference above. We have not
authorized anyone else to provide you with different information. You should not
assume that the information in this prospectus or any supplement or in the
documents incorporated by reference is accurate on any date other than the date
on the front of those documents.



                                       10
<PAGE>   14

                                     PART II
                     INFORMATION NOT REQUIRED IN PROSPECTUS


ITEM 14.       OTHER EXPENSES OF ISSUANCES AND DISTRIBUTION

        The following sets forth the costs and expenses, all of which shall be
borne by our company, in connection with the offering of the common stock
pursuant to this registration statement:

<TABLE>
               <S>                                   <C>
               SEC registration(1)                   $ 14,225
               Legal fees and expenses(2)              25,000
               Accounting fees and expenses(3)         27,000
               Miscellaneous                            1,000
                                                     --------
                       TOTAL                         $ 67,225
                                                     ========
</TABLE>

--------------

(1)  Includes $14,100 previously paid pursuant to Rule 457(c) in
     connection with the initial filing of this registration statement on
     October 13, 1999, Pre-Effective Amendment No. 1 filed on May 1, 2000 and
     Pre-Effective Amendment No. 2 filed on July 19, 2000.

(2)  Estimated. Includes approximately $21,000 in fees previously incurred in
     connection with the initial filing of this registration statement on
     October 13, 1999, Pre-Effective Amendment No. 1 filed on May 1, 2000 and
     Pre-Effective Amendment No. 2 filed on July 19, 2000.

(3)  Estimated. Includes approximately $23,000 in fees previously incurred in
     connection with the initial filing of this registration statement on
     October 13, 1999, Pre-Effective Amendment No. 1 filed on May 1, 2000 and
     Pre-Effective Amendment No. 2 filed on July 19, 2000.

ITEM 15.       INDEMNIFICATION OF DIRECTORS AND OFFICERS

        Our by-laws provide for indemnification of its directors and officers to
the fullest extent permitted by law. Insofar as indemnification for liabilities
under the Securities Act may be permitted to our directors or officers or
controlling persons of Epoch pursuant to our certificate of incorporation, as
amended, the by-laws and the Delaware General Corporation Law, we have been
informed that, in the SEC's opinion, this indemnification is against public
policy as expressed in the Securities Act and is therefore unenforceable.

        Section 102(b)(7) of the Delaware General Corporation Law provides that
a certificate of incorporation may include a provision which eliminates or
limits the personal liability of a director to the corporation or its
stockholders for monetary damages for breach of fiduciary duty as a director,
except for liability:

        -       for any breach of the director's duty of loyalty to the company
                or its stockholders,

        -       for acts or omissions not in good faith or which involve
                intentional misconduct or a knowing violation of law,

        -       under Section 174 of the Delaware General Corporation Law,
                relating to prohibited dividends or distributions or the
                repurchase or redemption of stock, or

        -       for any transaction from which the director derives an improper
                personal benefit.

        Our certificate of incorporation includes this kind of provision. As a
result of this provision, our company and its stockholders may be unable to
obtain monetary damages from a director for breach of his or her duty of care.



                                      II-1
<PAGE>   15

ITEM 16.       EXHIBITS AND FINANCIAL STATEMENT SCHEDULES

<TABLE>
<CAPTION>
   EXHIBIT NO.      DESCRIPTION
   -----------      -----------
   <S>              <C>
    5.1             Opinion of Stradling Yocca Carlson & Rauth, a Professional Corporation,
                    Counsel to Epoch (incorporated by reference to the exhibit 5.0 to Epoch's
                    Registration Statement on Form SB-2, No. 333-21353, filed February 7,
                    1997).

   23.2             Consent of Stradling Yocca Carlson & Rauth, a Professional
                    Corporation (included in the opinion filed as Exhibit 5.1).

   23.1             Consent of KPMG LLP, independent certified public accountants.

   24.1             Power of Attorney (included on the signature page).
</TABLE>



                                      II-2
<PAGE>   16

ITEM 17.       UNDERTAKINGS

        (a)    The undersigned registrant hereby undertakes:

               (1) To file, during any period in which it offers or sells
securities, a post-effective amendment to this registration statement to:

                        (iii) Include any material information with respect to
the plan of distribution not previously disclosed in this registration statement
or any material change to such information in the registration statement.

               (2) That, for the purpose of determining any liability under the
Securities Act of 1933, each such post-effective amendment shall be deemed to be
a new registration statement relating to the securities offered therein, and the
offering of such securities at that time shall be deemed to be the initial bona
fide offering thereof.

               (3) To remove from registration by means of a post-effective
amendment any of the securities being registered which remain unsold at the
termination of the offering.

        (b)    The undersigned registrant hereby undertake that, for purposes of
determining any liability under the Securities Act of 1933, each filing of the
registrant's annual report pursuant to Section 13(a) or Section 15(d) of the
Securities Exchange Act of 1934 (and, where applicable, each filing of an
employee benefit plan's annual report pursuant to Section 15(d) of the
Securities Exchange Act of 1934) that is incorporated by reference in the
registration statement shall be deemed to be a new registration statement
relating to the securities offered therein, and the offering of such securities
at that time shall be deemed to be the initial bona fide offering thereof.

        (c)    Insofar as indemnification for liabilities arising under the
Securities Act of 1933 may be permitted to directors, officers and controlling
persons of the registrants pursuant to the foregoing provisions, or otherwise,
the registrants have been advised that in the opinion of the Securities and
Exchange Commission such indemnification is against public policy as expressed
in the Act and is, therefore, unenforceable. In the event that a claim for
indemnification against such liabilities (other than the payment by the
registrants of expenses incurred or paid by a director, officer or controlling
person of the registrants in the successful defense of any action, suit or
proceeding) is asserted by such director, officer or controlling person in
connection with the securities being registered, the registrants will, unless in
the opinion of their counsel the matter has been settled by controlling
precedent, submit to a court of appropriate jurisdiction the question whether
such indemnification by it is against public policy as expressed in the Act and
will be governed by the final adjudication of such issue.



                                      II-3
<PAGE>   17

                                   SIGNATURES

        Pursuant to the requirements of the Securities Act, the registrant has
duly caused this registration statement to be signed on its behalf by the
undersigned, thereunto duly authorized, in the City of Redmond, State of
Washington, on the 28th day of December, 2000.


                                       EPOCH BIOSCIENCES, INC.



                                       By:   /s/ Sanford S. Zweifach
                                          --------------------------------------
                                          Sanford S. Zweifach
                                          President and Chief Financial Officer


        Pursuant to the requirements of the Securities Act, this registration
statement has been signed by the following persons in the capacities and on the
dates indicated.

<TABLE>
<CAPTION>
            Signature                              Title                             Date
            ---------                              -----                             ----
<S>                                 <C>                                        <C>
*                                   Chairman of the Board of Directors         December 28, 2000
-----------------------------       (Principal Executive Officer)
  Fred Craves, Ph.D.




*                                   Chief Executive Officer                    December 28, 2000
-----------------------------
  William G. Gerber, M.D.



/s/ Sanford S. Zweifach             President and Chief Financial              December 28, 2000
-----------------------------       Officer (Chief Accounting Officer)
  Sanford S. Zweifach


*                                   Director                                   December 28, 2000
-----------------------------
  Richard Dunning


*                                   Director                                   December 28, 2000
-----------------------------
  Herbert L. Heyneker.


*                                   Director                                   December 28, 2000
-----------------------------
  Kenneth L. Melmon, M.D.
</TABLE>



                                      II-4
<PAGE>   18

<TABLE>
<S>                                 <C>                                        <C>

*                                   Director                                   December 28, 2000
-----------------------------
  Riccardo Pigliucci



/s/ Sanford S. Zweifach                                                        December 28, 2000
-----------------------------
  *Sanford S. Zweifach
   As Attorney-in-Fact
</TABLE>



                                      II-5
<PAGE>   19

                                  EXHIBIT INDEX

<TABLE>
<CAPTION>
   EXHIBIT NO.      DESCRIPTION
   -----------      -----------
   <S>              <C>
    5.1             Opinion of Stradling Yocca Carlson & Rauth, a Professional Corporation,
                    Counsel to Epoch (incorporated by reference to the exhibit 5.0 to Epoch's
                    Registration Statement on Form SB-2, No. 333-21353, filed February 7,
                    1997).

   23.2             Consent of Stradling Yocca Carlson & Rauth, a Professional
                    Corporation (included in the opinion filed as Exhibit 5.1).

   23.1             Consent of KPMG LLP, independent certified public accountants.

   24.1             Power of Attorney (included on the signature page).
</TABLE>


                                     II-6



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