1

    As filed with the Securities and Exchange Commission on October 9, 2001
                                                      Registration No. 333-70134
================================================================================


                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                                AMENDMENT NO. 1
                                       TO
                                    FORM S-3
                             REGISTRATION STATEMENT
                                      UNDER
                           THE SECURITIES ACT OF 1933


                                   HYSEQ, INC.
             (EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER)


                                                 
          NEVADA                                        36-3855489
  (STATE OR OTHER JURISDICTION                        (I.R.S. EMPLOYER
OF INCORPORATION OR ORGANIZATION)                   IDENTIFICATION NUMBER)


                               675 ALMANOR AVENUE
                           SUNNYVALE, CALIFORNIA 94085
                                 (408) 524-8100
   (ADDRESS, INCLUDING ZIP CODE, AND TELEPHONE NUMBER, INCLUDING AREA CODE, OF
                    REGISTRANT'S PRINCIPAL EXECUTIVE OFFICES)

                                   TED W. LOVE
                      PRESIDENT AND CHIEF EXECUTIVE OFFICER
                                   HYSEQ, INC.
                               675 ALMANOR AVENUE
                           SUNNYVALE, CALIFORNIA 94085
                                 (408) 524-8100
 (NAME, ADDRESS, INCLUDING ZIP CODE, AND TELEPHONE NUMBER, INCLUDING AREA CODE,
                              OF AGENT FOR SERVICE)

                                    COPY TO:
                             ALAN C. MENDELSON, ESQ.
                                LATHAM & WATKINS
                             135 COMMONWEALTH DRIVE
                          MENLO PARK, CALIFORNIA 94025
                                 (650) 463-4693
        APPROXIMATE DATE OF COMMENCEMENT OF PROPOSED SALE TO THE PUBLIC:
As soon as practicable after the effective date of this registration statement.

    If the only securities being registered on this Form are pursuant to
dividend or interest reinvestment plans, 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 of
1933, other than securities offered only in connection with dividend or interest
reinvestment plans, check the following box. [X]

    If this Form is filed to register additional securities for an offering
pursuant to Rule 462(b) under the Securities Act, 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 delivery of the prospectus is expected to be made pursuant to Rule 434,
please check the following box. [ ]




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

        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 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.

   2

The information in this prospectus is not complete and may be changed. The
selling stockholder may not sell these securities until the registration
statement filed with the Securities and Exchange Commission is effective. This
prospectus is not an offer to sell these securities and the selling stockholder
is not soliciting offers to buy these securities in any state where the offer or
sale is not permitted.



                  SUBJECT TO COMPLETION, DATED OCTOBER 9, 2001



PROSPECTUS


                                4,561,101 SHARES

                                   HYSEQ, INC.


                                  COMMON STOCK

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


These shares of common stock are being offered by the selling stockholders
identified in this prospectus. The selling stockholders may sell their shares of
common stock in a number of different ways and at varying prices. We provide
more information about how the selling stockholders may sell their shares in the
section entitled "Plan of Distribution" beginning on page 3.

We are not selling any shares of our common stock under this prospectus and will
not receive any proceeds from the sale of these shares.

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


OUR COMMON STOCK IS QUOTED ON THE NASDAQ NATIONAL MARKET UNDER THE SYMBOL
"HYSQ." ON OCTOBER 8, 2001, THE LAST REPORTED SALE PRICE FOR OUR COMMON STOCK ON
THE NASDAQ NATIONAL MARKET WAS $8.42 PER SHARE.


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

INVESTING IN OUR COMMON STOCK INVOLVES RISKS. SEE "RISK FACTORS" BEGINNING ON
PAGE 1.

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

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.


                   , 2001



   3

                                TABLE OF CONTENTS



                                                                                         PAGE
                                                                                       
        Risk Factors.......................................................................1

        About Hyseq........................................................................1

        Special Note Regarding Forward-Looking Statements..................................1

        Use of Proceeds....................................................................1

        Selling Stockholders...............................................................2

        Plan of Distribution...............................................................3

        Legal Matters......................................................................5

        Experts............................................................................5

        Where You Can Find More Information................................................5


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

        You should rely only on the information we have provided or incorporated
by reference in this prospectus. Neither we nor the selling stockholders have
authorized anyone to provide you with additional or different information. The
selling stockholders are not making an offer of these securities in any
jurisdiction where the offer is not permitted. You should assume that the
information in this prospectus is accurate only as of the date on the front of
the document and that any information we have incorporated by reference is
accurate only as of the date of the document incorporated by reference. In this
prospectus, unless otherwise indicated, "Hyseq," "we," "us" or "our" refer to
Hyseq and its subsidiaries.

        We own or have rights to use trademarks or trade names that we use in
conjunction with the operation of our business. Hyseq is a registered trade and
service mark of the Company. All other trademarks, service marks and trade names
referred to in this Prospectus are the property of their respective owners.



                                        i
   4

                                  RISK FACTORS

        An investment in our common stock involves a high degree of risk. You
should consider carefully the risk factors contained in our most recent filing
on Form 10-K and all other information contained in and incorporated by
reference in this prospectus before making an investment decision. Additional
risks and uncertainties that are not yet identified or that we think are
immaterial may also materially harm our business, operating results and
financial condition and could result in a complete loss of your investment.

                                   ABOUT HYSEQ

        We are engaged in research and development of novel biopharmaceutical
products from our collection of proprietary genes discovered using our
high-throughput screening-by-hybridization platform. We believe our
screening-by-hybridization platform, which is related to our proprietary
sequencing-by-hybridization (SBH) technology, gives us a significant advantage
in discovering novel, rarely-expressed genes. We believe we possess one of the
most important proprietary databases of full-length human gene sequences. To
date, our activities have focused primarily on full-length gene sequencing,
patenting, bioinformatics and early stage research activities to prioritize our
therapeutic protein candidates. As of June 30, 2001, we had filed patent
applications on more than 7,100 full-length gene sequences. We are currently
investigating potential applications for two molecules, IL-1Hyl and CD39L4,
including potential applications for inflammatory diseases and for heart
disease. Meanwhile, we are expanding and accelerating our research activities to
elucidate the role of other novel genes in our proprietary database. Our
database includes genes which encode chemokines, growth factors, stem cell
factors, interferons, integrins, hormones, receptors and other potential protein
therapeutics or drug targets.

        We were incorporated in Illinois in August 1992 and reincorporated in
Nevada in November 1993. Our executive offices are located at 675 Almanor
Avenue, Sunnyvale, California 94085 and our telephone number is (408) 524-8100.
Our World Wide Web address is http://www.hyseq.com. Information contained in our
World Wide Web site should not be considered to be part of this prospectus.

                SPECIAL NOTE REGARDING FORWARD-LOOKING STATEMENTS

        Some of the statements in the section entitled "Risk Factors" and
elsewhere in this prospectus constitute forward-looking statements. These
statements involve known and unknown risks, uncertainties and other factors that
may cause our or our industry's results, levels of activity, or achievements to
be materially different from any future results, levels of activity or
achievements expressed or implied by such forward-looking statements. Such
factors include, among others, those listed under "Risk Factors" and elsewhere
in this prospectus.

        In some cases, you can identify forward-looking statements by
terminology such as "may," "will," "should," "intend," "expect," "plan,"
"anticipate," "believe," "estimate," "predict," "potential," or "continue," or
the negative of such terms or other comparable terminology.

        Although we believe that the expectations reflected in the
forward-looking statements are reasonable, we cannot guarantee future results,
events, levels of activity, performance or achievements. Except as may be
required by law, we undertake no obligation to publicly update any
forward-looking statements for any reason, even if new information becomes
available in the future.

                                 USE OF PROCEEDS

        We will not receive any of the proceeds from the sale of the shares of
common stock offered by the selling stockholders.



                                        1
   5

                              SELLING STOCKHOLDERS


        On August 28, 2001, we sold an aggregate of 3,040,733 shares of our
common stock to the selling stockholders in a private placement and issued the
selling stockholders warrants to purchase an aggregate of 1,520,368 shares of
common stock. In connection with this sale, we agreed to file a registration
statement with the SEC covering the resale of the shares, including the shares
issuable upon exercise of the warrants. The following table sets forth the names
of the selling stockholders, the number of shares of our common stock that each
selling stockholder beneficially owns as of September 21, 2001 and the number of
shares which may be offered pursuant to this prospectus. Beneficial ownership is
determined in accordance with Rule 13d-3 under the Securities Exchange Act of
1934. No selling stockholder may exercise its warrant if such exercise would
result in the selling stockholder owning more than 4.999% of our outstanding
shares of common stock (including for such purpose the shares of common stock
issuable upon such exercise). Percentage ownership is based on 19,103,574 shares
of common stock outstanding as of October 4, 2001. Each selling stockholder
may sell all, some or none of the common stock being offered.




                                                                              SHARES BENEFICIALLY
                                                SHARES          SHARES         OWNED SUBSEQUENT
                                             BENEFICIALLY     OFFERED BY      TO THE OFFERING (1)
NAME OF SELLING STOCKHOLDER                 OWNED PRIOR TO       THIS       ----------------------
---------------------------                  THE OFFERING     PROSPECTUS     SHARES      PERCENT
                                            --------------    ----------    -------      ---------
                                                                             
Blue Ridge Limited Partnership                 428,573         428,573           0           *
Cranshire Capital, L.P.                        353,573         353,573           0           *
Euram Cap. Strat. (A) Fund Ltd.                 75,000          75,000           0           *
Narragansett I, LP                             328,821         328,821           0           *
Narragansett Offshore, Ltd.                    667,607         667,607           0           *
SDS Merchant Fund, L.P.                        150,000         150,000           0           *
Peter S. Garcia(2)                              21,735          21,435          300          *
Pine Ridge Financial, Inc.                     576,858         567,858           0           *
The Rathmann Family 1989 Revocable
Trust(2)                                     3,613,078         857,142       2,755,936     14.4
Richard G. Robb                                137,500          37,500        100,000        *
Swiftcurrent Partners, L.P.                    214,287         214,287           0           *
Ted W. Love(2)                                 260,903          21,435        239,468       1.3
Vulcan Ventures Inc.                           750,000         750,000           0           *
Vertical Ventures, LLC                          21,435          21,435           0           *
William Bennett(2)                              27,435          21,435         6,000         *
Weist Family Trust(2)                          251,675          45,000        206,675       1.1

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

*       Less than 1% of the outstanding shares of common stock.

(1)     Assumes the sale of all shares, including shares issuable upon exercise
of the warrants, offered hereby.

(2)     These selling stockholders have agreed, pursuant to ongoing discussions
that we are having with the NASD, not to vote or transfer their shares of common
stock offered pursuant to this prospectus until such time as the offer and sale
of the shares to them in the private placement has been ratified by our
stockholders.



                                        2
   6

        William F. Bennett, Ph.D. has served as our Senior Vice President
Research since July 2001.

        Peter S. Garcia has served as our Senior Vice-President and Chief
Financial Officer since May 2001.

        Ted W. Love, M.D. has served as our President and Chief Executive
Officer since March 2001, and as a director since February 2001. Dr. Love served
as our President and Chief Operating Officer from January 2001 until March 2001.

        George B. Rathmann, Ph.D. has served as Chairman and a director since
February 2000. Dr. Rathmann served as our Chief Executive Officer from May 2000
to March 2001, and also served as our President from May 2000 to January 2001.
We have entered into a Line of Credit Agreement, dated as of August 6, 2001,
with Dr. Rathmann, which provides us with a credit line of up to an aggregate
principal amount of $20 million, with interest on outstanding principal amounts
at a rate per annum equal to one percent (1%) above the prime rate most recently
announced by Bank of America National Trust and Savings Association. We can
repay borrowings under the credit line with shares of our common stock. In
November 2000, we entered into another $20 million line of credit with Dr.
Rathmann, which we completely drew down in March 2001 and repaid by issuing
2,237,637 shares of our common stock.

        Robert D. Weist has served as a director since May 1993 and as Vice
Chairman since February 2000. Mr. Weist served as Chairman from March 1994 until
February 2000 and as President from May 1993 until March 1994. Mr. Weist and his
spouse serve as co-trustees of the Weist Family Trust.

        Except as stated above, we are unaware of any material relationship
between the selling stockholders and us in the past three years other than as a
result of the ownership of shares of our common stock.

        We are registering the shares of our common stock offered by the selling
stockholders pursuant to contractual registration rights we granted to the
selling stockholders. We have filed a registration statement related to the
shares offered hereby and have agreed to keep such registration statement
effective until the earlier of (1) the date on which all the shares have been
sold or may be sold without volume restrictions pursuant to Rule 144(k) under
the Securities Act, and (2) two years after the registration statement is
declared effective.

        We will pay the registration and filing fees, printing expenses, listing
fees, blue sky fees, if any, and fees and disbursements of our counsel in
connection with this offering, but the selling stockholders will pay any
underwriting discounts, selling commissions and similar expenses relating to the
sale of the shares. In addition, we have agreed to indemnify the selling
stockholders against certain liabilities, including liabilities under the
Securities Act, in connection with this offering. The selling stockholders have
agreed to indemnify us and our directors and officers, as well as any person
that controls us, against certain liabilities, including liabilities under the
Securities Act.

                              PLAN OF DISTRIBUTION

        The selling stockholders and any of their pledges, assignees and
successors-in-interest may, from time to time, sell any or all of their shares
of Common Stock on any stock exchange, market or trading facility on which the
shares are traded or in private transactions. These sales may be at fixed or
negotiated prices. The selling stockholders may use any one or more of the
following methods when selling shares:

        -   ordinary brokerage transactions and transactions in which the
            broker-dealer solicits purchasers;



                                        3
   7

        -   block trades in which the broker-dealer will attempt to sell the
            shares as agent but may position and resell a portion of the block
            as principal to facilitate the transaction;

        -   purchases by broker-dealer as principal and resale by the
            broker-dealer for its account;

        -   an exchange distribution in accordance with the rules of the
            applicable exchange;

        -   privately negotiated transactions;

        -   short sales;

        -   broker-dealers may agree with the selling stockholders to sell a
            specified number of such shares at a stipulated price per share;

        -   a combination of any such methods of sale; and

        -   any other method permitted pursuant to applicable law.

        The selling stockholders may also sell shares under Rule 144 under the
Securities Act, if available, rather than under this prospectus.

        Broker-dealers engaged by the selling stockholders may arrange for other
broker-dealers to participate in sales. Broker-dealers may receive commissions
or discounts from the selling stockholders (or, if any broker-dealer acts as
agent for the purchaser of shares, from the purchaser) in amounts to be
negotiated. The selling stockholders do not expect these commissions and
discounts to exceed what is customary in the types of transactions involved.

        The selling stockholders may from time to time pledge or grant a
security interest in some or all of the Shares or common stock or Warrants owned
by them and, if they default in the performance of their secured obligations,
the pledgees or secured parties may offer and sell the shares of common stock
from time to time under this prospectus, or under an amendment to this
prospectus under Rule 424(b)(3) or other applicable provision of the Securities
Act of 1933 amending the list of selling stockholders to include the pledgee,
transferee or other successors in interest as selling stockholders under this
prospectus.

        The selling stockholders also may transfer the shares of common stock in
other circumstances, in which case the transferees, pledgees or other successors
in interest will be the selling beneficial owners for the purposes of this
prospectus.

        The selling stockholders and any broker-dealers or agents that are
involved in selling the shares may be deemed to be "underwriters" within the
meaning of the Securities Act in connection with such sales. In such event, any
commissions received by such broker-dealers or agents and any profit on the
resale of the shares purchased by them may be deemed to be underwriting
commissions or discounts under the Securities Act. The selling stockholders have
informed the Company that they do not have any agreement or understanding,
directly or indirectly, with any person to distribute the Common Stock.

        We have advised the selling stockholders that they are required to
comply with Regulation M promulgated under the Securities and Exchange Act
during such time as they may be engaged in a distribution of the shares. With
some exceptions, Regulation M precludes any selling stockholder, any affiliated
purchaser and any broker-dealer or other person who participates in such
distribution from bidding for or purchasing, or attempting to induce any person
to bid for or purchase any security that is the subject of the distribution
until the entire distribution is complete. Regulation M also prohibits any bids
or purchases made in order to stabilize the price of a security in connection
with the distribution of that security. All of the foregoing may affect the
marketability of the common stock.



                                        4
   8

        We are required to pay all fees and expenses incident to the
registration of the shares, including $10,000 of fees and disbursements of
counsel to the selling stockholders. We have agreed to indemnify the selling
stockholders against certain losses, claims, damages and liabilities, including
liabilities under the Securities Act.

                                  LEGAL MATTERS

        Kummer Kaempfer Bonner & Renshaw of Las Vegas, Nevada will issue an
opinion about certain legal matters with respect to the common stock being
offered in this prospectus.

                                     EXPERTS


        The financial statements of Hyseq Inc. and subsidiaries as of December
31, 2000 and for the year then ended have been incorporated by reference herein
and in the registration statement in reliance upon the report of KPMG LLP,
independent auditors, incorporated by reference herein, and upon the authority
of said firm as experts in accounting and auditing.

        Ernst & Young LLP, independent auditors, have audited our consolidated
balance sheet as of December 31, 1999, and the related consolidated statements
of operations, stockholders' equity and cash flows for each of the two years in
the period ended December 31, 1999, as set forth in their report, which is
incorporated by reference in this prospectus and elsewhere in the registration
statement. These financial statements are included in reliance upon such report
given on the authority of such firm as experts in accounting and auditing.


                       WHERE YOU CAN FIND MORE INFORMATION

        We are a reporting company and file annual, quarterly and current
reports, proxy statements and other information with the Securities and Exchange
Commission, or the SEC. You may read and copy these reports, proxy statements
and other information at the SEC's public reference rooms at 450 Fifth Street,
N.W., Washington, D.C., 20549, as well as at the SEC's regional office at 500
West Madison Street, Suite 1400, Chicago, Illinois, 60661. You can request
copies of these documents by writing to the SEC and paying a fee for the copying
cost. Please call the SEC at 1-800-SEC-0330 for more information about the
operation of the public reference rooms. Our SEC filings are also available at
the SEC's Web site at "http://www.sec.gov". In addition, you can read and copy
our SEC filings at the office of the National Association of Securities Dealers,
Inc. at 1735 K Street, Washington, D.C. 20006.

        The SEC allows us to "incorporate by reference" information that we file
with them, which means that we can disclose important information to you by
referring you to those documents. The information incorporated by reference is
an important part of this prospectus, and information that we file later with
the SEC will automatically update and supersede this information. Further, all
filings we make under the Securities Exchange Act after the date of the initial
registration statement and prior to effectiveness of the registration statement
shall be deemed to be incorporated by reference into this prospectus. We
incorporate by reference the documents listed below and any future filings we
will make with the SEC under Section 13(a), 13(c), 14 or 15(d) of the Securities
Exchange Act of 1934:

        1. Our Annual Report on Form 10-K for the year ended December 31, 2000,
filed with the SEC on April 2, 2001;

        2. Our Quarterly Reports for the quarters ended March 31, 2001 and June
30, 2001, filed with the SEC on May 15, 2001 and August 14, 2001;

        3. Our Current Reports on Form 8-K, filed with the SEC on January 17,
2001, February 21, 2001, March 23, 2001, May 3, 2001, May 21, 2001, July 20,
2001 and September 12, 2001.



                                        5
   9

        4. The description of our common stock set forth in our Registration
Statement on Form 8-A, filed with the SEC on July 23, 1997.

        We will provide to you at no cost a copy of any and all of the
information incorporated by reference into the registration statement of which
this prospectus is a part. You may make a request for copies of this information
in writing or by telephone. Requests should be directed to:

                                   Hyseq, Inc.
                           Attention: Peter S. Garcia
                               675 Almanor Avenue
                               Sunnyvale, CA 94085
                                 (408) 524-8100



                                        6
   10

                                     PART II

                     INFORMATION NOT REQUIRED IN PROSPECTUS

ITEM 14. OTHER EXPENSES OF ISSUANCE AND DISTRIBUTION


                                                                   
        Securities and Exchange Commission Registration Fee            $8,362.02

        Nasdaq National Market Listing Fee                            $17,500.00

        Legal Fees and Expenses                                       $35,000.00

        Accountants' Fees and Expenses                                $13,000.00

        Miscellaneous                                                 $10,037.98

                Total                                                 $83,900.00
                                                                       =========


        The foregoing items, except for the Securities and Exchange Commission
Registration Fee, are estimated.

ITEM 15. INDEMNIFICATION OF DIRECTORS AND OFFICERS

        Pursuant to the provisions of Section 78.7502 of the Nevada General
Corporation Law, every Nevada corporation has authority to indemnify any person
who was or is a party or is threatened to be made a party to any threatened,
pending or completed action, suit or proceeding, except an action by or in the
right of the corporation, by reason of the fact that such person is or was a
director, officer, employee or agent of the corporation, or is or was serving at
the request of the corporation as a director, officer, employee or agent of
another corporation, partnership, joint venture, trust or other enterprise,
against expenses, including attorneys' fees, judgments, fines and amounts paid
in settlement actually and reasonably incurred in connection with the action,
suit or proceeding if such person acted in good faith and in a manner which such
person reasonably believed to be in or not opposed to the best interest of the
corporation, and, with respect to any criminal action or proceeding, had no
reasonable cause or belief his conduct was unlawful.

        Pursuant to the provisions of Section 78.7502, every Nevada corporation
also has the authority to indemnify any person who was or is a party or is
threatened to be made a party to any threatened, pending or completed action or
suit by or in the right of the corporation to procure a judgment in its favor by
reason of the fact that such person is or was a director, officer, employee or
agent of the corporation, or is or was serving at the request of the corporation
as a director, officer, employee or agent of another corporation, partnership,
joint venture, trust or other enterprise against expenses including amounts paid
in settlement and attorneys' fees actually and reasonably incurred by such
person in connection with the defense or settlement of the action or suit if
such person acted in good faith and in a manner which such person reasonably
believed to be in or not opposed to the best interests of the corporation. No
indemnification shall be made, however, for any claim, issue or matter as to
which a person has been adjudged by a court of competent jurisdiction to be
liable to the corporation or for amounts paid in settlement to the corporation,
unless and only to the extent that the court determines that in view of all the
circumstances, the person is fairly and reasonably entitled to indemnity for
such expenses as the court deems proper.



                                      II-1
   11

        To the extent any person referred to in the two immediately preceding
paragraphs is successful on the merits or otherwise in defense of any action,
suit or proceeding, the Nevada General Corporation Law provides that such person
must be indemnified by the corporation against expenses including attorneys'
fees, actually and reasonably incurred by him in connection with the defense.

        Section 78.751 of the Nevada General Corporation Law requires the
corporation to obtain a determination that any discretionary indemnification is
proper under the circumstances. Such a determination must be made by the
corporation's stockholders; its board of directors by majority vote of a quorum
consisting of directors who were not parties to the action, suit or proceeding;
or under certain circumstances, by independent legal counsel. Our Amended and
Restated Bylaws provide that we shall indemnify our directors, officers,
employees and agents to the fullest extent provided by the Nevada General
Corporation Law.

        In addition, Section 78.037 of the Nevada General Corporation Law
permits Nevada corporations to include in their articles of incorporation a
provision eliminating the personal liability of their directors and officers to
the corporation or stockholders for damages resulting from their breach of
fiduciary duties, other than any liability for (i) acts or omissions involving
intentional misconduct, fraud or a knowing violation of law, or (ii) unlawful
distributions. Our Amended and Restated Articles of Incorporation contain such a
provision.

        We have entered into indemnification agreements with each of our
officers and directors in which we agree to indemnify and hold harmless the
officer or director to the fullest extent permitted by applicable law in
connection with any threatened, pending or completed action, suit or proceeding,
or any inquiry or investigation not initiated by the officer or director, by
reason of the fact that such person is or was a director, officer, employee,
agent or fiduciary of us, or is or was serving at our request as a director,
officer, employee, agent or fiduciary of another corporation, partnership, joint
venture, trust, employee benefit plan or other enterprise, against any and all
expenses, judgments, penalties, fines and settlement amounts actually and
reasonably incurred by such officer or director or on his or her behalf
(including mandatory advancement of expenses), if such person acted in good
faith and in a manner which such person believed to be or not opposed to our
best interests. The indemnification agreements set forth procedures that apply
in the event of a claim for indemnification thereunder.

        We also maintain insurance to protect ourself and our directors,
officers, employees and agents against expenses, liabilities and losses incurred
by such persons in connection with their service in the foregoing capacities.

ITEM 16. EXHIBITS




   EXHIBIT NO.                              DESCRIPTION OF DOCUMENT
                
       3.1         Amended and Restated Articles of Incorporation of Hyseq, Inc., including
                   Amendment No. 1 and Amendment No. 2 thereto.(1)

      *3.2         Amendment No. 3 to Amended and Restated Articles of Incorporation of
                   Hyseq, Inc.

       3.3         Amended and Restated By-Laws of Hyseq, Inc.(2)

       4.1         Specimen Common Stock certificate.(3)

       4.2         Rights Agreement between Hyseq, Inc. and U.S. Stock Transfer, dated June 5,
                   1998.(4)

      *4.3         Form of Securities Purchase Agreement, dated as of August 28, 2001, by
                   and among Hyseq, Inc. and the investors party thereto.





                                      II-2
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   EXHIBIT NO.                              DESCRIPTION OF DOCUMENT
                
      *4.4         Form of Registration Rights Agreement, dated as of August 28, 2001, by
                   and among Hyseq, Inc. and the investors party thereto.

      *4.5         Form of Warrant, dated as of August 28, 2001.

      *5.1         Opinion of Kummer Kaempfer Bonner & Renshaw.

      23.1         Consent of KPMG LLP, Independent Auditors.

      23.2         Consent of Ernst & Young LLP, Independent Auditors.

     *23.3         Consent of Kummer Kaempfer Bonner & Renshaw.

     *24.1         Power of Attorney.


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

 *  Previously filed.


(1) Incorporated by reference to our Registration Statement filed on Form S-1,
File No. 333-29091, filed on June 12, 1997.

(2) Incorporated by reference to our Annual Report on Form 10-K for the fiscal
year ended December 31, 2000, filed on April 2, 2001.

(3) Incorporated by reference to our Registration Statement filed on Form S-1,
File No. 333-29091, filed on June 12, 1997.

(4) Incorporated by reference to our Current Report on Form 8-K, filed on July
31, 1998.


ITEM 17. UNDERTAKINGS

        The undersigned registrant hereby undertakes:

        (1) To file, during any period in which offers or sales are being made
pursuant to this registration statement, a post-effective amendment to this
registration statement: (i) To include any prospectus required by Section
10(a)(3) of the Securities Act of 1933; (ii) To reflect in the prospectus any
facts or events arising after the effective date of the registration statement
(or the most recent post-effective amendment thereof) which, individually or in
the aggregate, represent a fundamental change in the information set forth in
the registration statement. Notwithstanding the foregoing, any increase or
decrease in volume of securities offered (if the total dollar value of
securities offered would not exceed that which was registered) and any deviation
from the low or high end of the estimated maximum offering range may be
reflected in the form of prospectus filed with the Commission pursuant to Rule
424(b) if, in the aggregate, the changes in volume and price represent no more
than a 20 percent change in the maximum aggregate offering price set forth in
the "Calculation of Registration Fee" table in the effective registration
statement; (iii) To include any material information with respect to the plan of
distribution not previously disclosed in the 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; and

        (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.

        The undersigned registrant hereby undertakes that, for the purposes of
determining any liability under the Securities Act of 1933, each filing of the
registrant's annual report pursuant to Section 13(a) of



                                      II-3
   13

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.

        Insofar as indemnification for liabilities arising under the Securities
Act of 1933 may be permitted to directors, officers, and controlling persons of
the registrant pursuant to the provisions described in Item 15, or otherwise,
the registrant has 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
registrant of expenses incurred or paid by a director, officer, or controlling
person of the registrant 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 registrant will, unless in
the opinion of its 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.


                                   SIGNATURES



        Pursuant to the requirements of the Securities Act of 1933, the
registrant certifies that it has reasonable grounds to believe that it meets all
of the requirements for filing on Form S-3 and has duly caused this registration
statement on Form S-3 to be signed on its behalf by the undersigned, thereunto
duly authorized, in the City of Sunnyvale, State of California, on the 8th day
of October, 2001.


                                  HYSEQ, INC.

                                  By: /s/ DR. TED W. LOVE
                                     -----------------------------------------
                                         Dr. Ted W. Love
                                         President and Chief Executive Officer




        Pursuant to the requirements of the Securities Act of 1933, as amended,
this registration statement on form S-3 has been signed below by the following
persons in the capacities and on the dates indicated.



                                      II-4
   14




         SIGNATURE                              TITLE                        DATE
         ---------                              -----                        ----
                                                                  
                                    President and Chief Executive       October 8, 2001
     /s/ Dr. Ted W. Love                       Officer
 ------------------------------     (Principal Executive Officer)
       Dr. Ted W. Love


                                      Senior Vice President and         October 8, 2001
               *                       Chief Financial Officer
 ------------------------------       (Principal Financial and
        Peter S. Garcia                  Accounting Officer)


               *                       Chairman of the Board of         October 8, 2001
 ------------------------------              Directors
     George B. Rathmann


               *                      Vice Chairman of the Board        October 8, 2001
 ------------------------------            of Directors
       Robert D. Weist


               *                             Director                   October 8, 2001
------------------------------
      Dr. Raymond F. Baddour


               *                             Director                   October 8, 2001
 ------------------------------
     Dr. Radoje Drmanac


               *                             Director                   October 8, 2001
 ------------------------------
     Thomas N. McCarter


               *                             Director                   October 8, 2001
 ------------------------------
         Dr. Ernst Schweizer

*By:    /s/ Dr. Ted W. Love
    ---------------------------
            Dr. Ted W. Love
           ATTORNEY-IN-FACT





                                      II-5
   15

                                INDEX TO EXHIBITS




   EXHIBIT NO.                              DESCRIPTION OF DOCUMENT
                
       3.1         Amended and Restated Articles of Incorporation of Hyseq, Inc., including
                   Amendment No. 1 and Amendment No. 2 hereto.(1)

      *3.2         Amendment No. 3 to Amended and Restated Articles of Incorporation of
                   Hyseq, Inc.

       3.3         Amended and Restated By-Laws of Hyseq, Inc.(2)

       4.1         Specimen Common Stock certificate.(3)

       4.2         Rights Agreement between Hyseq, Inc. and U.S. Stock Transfer dated June 5,
                   1998.(4)

      *4.3         Form of Securities Purchase Agreement, dated as of August 28, 2001, by
                   and among Hyseq, Inc. and the investors party thereto.

      *4.4         Form of Registration Rights Agreement, dated as of August 28, 2001, by
                   and among Hyseq, Inc. and the investors party thereto.

      *4.5         Form of Warrant, dated as of August 28, 2001.

      *5.1         Opinion of Kummer Kaempfer Bonner & Renshaw.

      23.1         Consent of KPMG LLP, Independent Auditors.

      23.2         Consent of Ernst & Young LLP, Independent Auditors.

     *23.3         Consent of Kummer Kaempfer Bonner & Renshaw.

     *24.1         Power of Attorney.


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

 *  Previously filed.


(1) Incorporated by reference to our Registration Statement filed on Form S-1,
File No. 333-29091, filed on June 12, 1997.

(2) Incorporated by reference to our Annual Report on Form 10-K for the fiscal
year ended December 31, 2000, filed on April 2, 2001.

(3) Incorporated by reference to our Registration Statement filed on Form S-1,
File No. 333-29091, filed on June 12, 1997.

(4) Incorporated by reference to our Current Report on Form 8-K, filed on July
31, 1998.



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