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                           SCHEDULE 14A (RULE 14a-101)

                     INFORMATION REQUIRED IN PROXY STATEMENT

                            SCHEDULE 14A INFORMATION
                PROXY STATEMENT PURSUANT TO SECTION 14(a) OF THE
              SECURITIES EXCHANGE ACT OF 1934 (AMENDMENT NO. _____)

Filed by the Registrant [X]

Filed by a Party other than the Registrant [ ]

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                                             Commission Only (as permitted by
                                             Rule 14a-6(e)(2))

[X]   Definitive Proxy Statement

[ ]   Definitive Additional Materials

[ ]   Soliciting Material Pursuant to Rule 14a-11(c) or Rule 14a-12


                           Axys Pharmaceuticals, Inc.
- --------------------------------------------------------------------------------
                (Name of Registrant as Specified in its Charter)


- --------------------------------------------------------------------------------
    (Name of Person(s) Filing Proxy Statement, if other than the Registrant)


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                                  [AXYS.LOGO]

                           AXYS PHARMACEUTICALS, INC.

                                180 KIMBALL WAY
                     SOUTH SAN FRANCISCO, CALIFORNIA 94080


                                 April 16, 2001


Dear Stockholders,

     I am pleased to invite you to attend our annual meeting of stockholders to
be held at 9:00 a.m. on Monday, May 14, 2001, at Axys' headquarters located at
180 Kimball Way, South San Francisco, California.

     Legal documents are often times confusing, so this year we decided again to
write a jargon-free "plain English" proxy notice and proxy statement. With this
letter we are including the notice for our annual meeting, the proxy statement,
the proxy card and the 2000 annual report. We hope you find its simplified
format helpful and we welcome your comments.

     Your vote is important to us and I look forward to seeing you on May 14.
Whether you plan to attend the annual meeting in person or not, I hope you will
vote as soon as possible.

                                          Sincerely,

                                          /s/ Paul J. Hastings
                                          Paul J. Hastings
                                          President and Chief Executive Officer
   3

                           AXYS PHARMACEUTICALS, INC.
                                180 KIMBALL WAY
                     SOUTH SAN FRANCISCO, CALIFORNIA 94080
                                 (650) 829-1000
                            ------------------------

                    NOTICE OF ANNUAL MEETING OF STOCKHOLDERS
                       TO BE HELD ON MONDAY, MAY 14, 2001

TIME:                   9:00 a.m.

PLACE:                  Axys Pharmaceuticals' Headquarters
                        180 Kimball Way
                        South San Francisco, California 94080

MATTERS TO BE VOTED ON: (1) To elect the Board of Directors;

                        (2) To approve a 1,500,000 share increase in the number
                            of shares of common stock issuable under Axys' 1997
                            Equity Incentive Plan;

                        (3) To amend Axys' Certificate of Incorporation to
                            increase the number of authorized shares of common
                            stock by 50,000,000 shares;

                        (4) To ratify the appointment of Ernst & Young LLP as
                            Axys' independent auditors; and

                        (5) To transact any other business properly coming
                            before the meeting.

RECORD DATE:            You may vote at the meeting if you were a stockholder at
                        the close of business on Monday, April 9, 2001, the
                        record date. If on April 9, 2001, your shares were held
                        of record in your brokerage firm or another similar
                        organization, you may vote at the annual meeting if you
                        obtain a valid proxy card from them issued in your name.

VOTING BY PROXY:        Please return your proxy as soon as possible so that
                        your shares can be voted at the meeting in accordance
                        with your instructions. For more instructions, please
                        see the Questions and Answers beginning on page 1 of
                        this proxy statement and the instructions on the proxy
                        card.

                                          By Order of the Board of Directors,

                                          /s/ DOUGLAS H. ALTSCHULER

                                          Douglas H. Altschuler
                                          Vice President and General Counsel


April 16, 2001


                            YOUR VOTE IS IMPORTANT.
TO VOTE YOUR SHARES, PLEASE SIGN, DATE AND COMPLETE THE ENCLOSED PROXY AND MAIL
                  IT PROMPTLY IN THE ENCLOSED RETURN ENVELOPE.
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                               TABLE OF CONTENTS




                                                              PAGE
                                                              ----
                                                           
Questions and Answers about this Proxy Material and the
  Annual Meeting............................................    1
Proposals to be Voted Upon..................................    5
Nominees for Directors......................................    6
Board Committees............................................    7
Compensation of Non-employee Directors......................    8
Stock Ownership of Beneficial Owners, Directors and
  Management................................................    9
Compensation of Executive Officers..........................   11
Report of the Compensation Committee........................   17
General Description of the 1997 Equity Incentive Plan.......   21
Amendment to Axys' Certificate of Incorporation.............   25
Audit Committee Report......................................   27
Appointment of Independent Accountants......................   28
Section 16(a) Beneficial Ownership Reporting Compliance.....   28
Relationships and Transactions you should know about........   28
Performance Graph...........................................   29
Other Matters...............................................   29
Appendix A -- Audit Committee Charter.......................  A-1
Appendix B -- Certificate of Amendment to Certificate of
  Incorporation.............................................  B-1
Appendix C -- Directions to Axys............................  C-1



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                QUESTIONS AND ANSWERS ABOUT THIS PROXY MATERIAL
                             AND THE ANNUAL MEETING

WHY AM I RECEIVING THESE MATERIALS?


     The Board of Directors (the "Board") of Axys Pharmaceuticals, Inc.
(sometimes referred to as the "Company" or "Axys") is providing these proxy
materials for you in connection with Axys' annual meeting of stockholders which
will take place on May 14, 2001. You are invited to attend the meeting and are
requested to vote on the proposals described in this proxy statement. The
Company intends to mail this proxy statement and accompanying proxy card on or
about April 17, 2001, to all stockholders of record entitled to vote at the
annual meeting.


WHO MAY ATTEND THE MEETING?

     All Axys stockholders are invited to attend, including stockholders whose
shares are held by their brokerage firm or another similar organization.

WHAT INFORMATION IS CONTAINED IN THESE MATERIALS?

     The information included in this proxy statement relates to the proposals
to be voted on at the annual meeting, the voting process, the compensation of
directors and our most highly paid officers, and certain other required
information. Our 2000 Annual Report is also enclosed.

WHO IS PAYING FOR THIS PROXY'S SOLICITATION PROCESS?

     The enclosed proxy is solicited on behalf of the Board and Axys is paying
for the entire cost of the proxy voting process. Copies of this material will be
given to banks, brokerage houses and other institutions that hold Axys' stock
that is beneficially owned by others. Axys will reimburse these banks, brokerage
houses and other institutions for their reasonable out of pocket expenses in
forwarding these proxy materials to stockholders who are beneficial owners.
Original solicitation of proxies by mail may be supplemented by telephone,
telegram, or personal solicitation by directors, officers, or other employees of
Axys and by MacKenzie Partners. No additional compensation will be paid to
directors, officers or other Axys employees for soliciting proxies, but
MacKenzie Partners may be paid its customary fee of approximately $5,500 plus
out-of-pocket expenses.

WHAT AM I VOTING ON?

     There are four known matters to be voted on at the annual meeting:


     - the election of seven nominees to our Board of Directors;


     - a proposed 1,500,000 share increase in the number of shares of common
       stock authorized to be issued under the Company's 1997 Equity Incentive
       Plan;

     - a proposed amendment to the Certificate of Incorporation to increase the
       number of authorized shares of the Company's common stock by 50,000,000
       shares; and

     - the ratification of Ernst & Young LLP as the Company's independent
       auditors for 2001.

WHAT ARE THE BOARD'S VOTING RECOMMENDATIONS?

     Our Board of Directors recommends that you vote your shares "FOR" each of
the Board's nominees to the Board of Directors and "FOR" each of the other
proposals.

WHO CAN VOTE AT THE ANNUAL MEETING?


     Stockholders of record at the close of business on April 9, 2001 (the
"Record Date"). Also, if on April 9, 2001 your shares were held in the name of
your brokerage firm, you may vote at the annual meeting if you obtain a valid
proxy from them in your name. On each matter to be considered at the annual
meeting, each


                                        1
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stockholder will be entitled to cast one vote for each share of the Company's
common stock held of record by such stockholder on the Record Date.


WHAT IS THE DIFFERENCE BETWEEN HOLDING SHARES AS A STOCKHOLDER OF RECORD AND AS
A BENEFICIAL OWNER?

     Most Axys stockholders hold their shares in an account at a brokerage firm,
bank or other nominee holder, rather than holding share certificates directly in
the stockholder's own name. As summarized below, there are some distinctions
between shares held of record and those owned beneficially.

  Stockholder of Record

     If on April 9, 2001 your shares were registered directly in your name with
Axys' transfer agent, CompuShare Investor Services, Inc., you are a stockholder
of record who may vote at the annual meeting and these proxy materials are being
sent directly to you by Axys. As the stockholder of record, you have the right
to direct the voting of your shares by returning the enclosed proxy card to Axys
or to vote in person at the meeting. Whether or not you plan to attend the
meeting, please complete, date and sign the enclosed proxy card to ensure that
your vote is counted. Each share is entitled to one vote for each item to be
voted on.

  Beneficial Owner

     If on April 9, 2001 your shares were held in an account at a brokerage firm
or at a bank or other nominee holder, you are considered the beneficial owner of
shares held "in street name" and these proxy materials are being forwarded to
you by your broker or nominee who is considered the stockholder of record for
the purposes of voting at the annual meeting. As the beneficial owner, you have
the right to direct your broker on how to vote your shares and are also invited
to attend the annual meeting. However, since you are not the stockholder of
record, you may not vote these shares in person at the annual meeting unless you
receive a valid proxy from your brokerage firm, bank or other nominee holder. To
obtain a valid proxy, you must make a special request of your brokerage firm,
bank or other nominee holder. If you do not make this request, you can still
vote by a voting instruction card enclosed for you to use.

HOW MANY VOTES MUST THE BOARD NOMINEES RECEIVE TO BE ELECTED?

     The seven nominees receiving the highest number of "yes" votes will be
elected as directors. This number is called a plurality.

WHAT HAPPENS IF A NOMINEE IS UNABLE TO STAND FOR RE-ELECTION?

     The Board may, by vote, decide on reducing the size of the Board or name a
substitute nominee. If a substitute is named, shares represented by proxies may
be voted for a substitute nominee.

HOW MANY VOTES MUST THE 1,500,000 SHARE INCREASE FOR THE 1997 EQUITY INCENTIVE
PLAN RECEIVE IN ORDER TO BE APPROVED?


     In order to be approved, the proposal to increase the number of shares
issuable pursuant to the 1997 Equity Incentive Plan shares must receive a "yes"
vote of a majority of the shares present in person or represented by valid
proxies at the meeting and entitled to vote on the matter.


HOW MANY VOTES MUST THE AMENDMENT TO THE COMPANY'S CERTIFICATE OF INCORPORATION
TO INCREASE THE NUMBER OF AUTHORIZED SHARES OF COMMON STOCK BY 50,000,000 SHARES
RECEIVE IN ORDER TO BE APPROVED?


     In order to be approved, the proposal to amend the Company's Certificate of
Incorporation to increase the number of authorized shares of common stock by
50,000,000 shares must receive a "yes" vote of a majority of the shares present
in person or represented by valid proxies at the meeting and entitled to vote on
the matter.


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HOW MANY VOTES MUST THE RATIFICATION OF APPOINTMENT OF INDEPENDENT AUDITORS
RECEIVE IN ORDER TO BE APPROVED?


     The ratification of the appointment of Ernst & Young LLP as the Company's
auditors for the fiscal year ending December 31, 2001 must receive a "yes" vote
of a majority of the shares present in person or represented by valid proxies at
the meeting and entitled to vote on the matter. In the event the stockholders
fail to ratify the appointment, the Board will reconsider its selection. Even if
the selection is ratified, the Board in its discretion may direct the
appointment of a different independent accounting firm at any time during the
year if the Board feels that such a change would be in the best interest of the
Company and its stockholders.


HOW ARE THE VOTES COUNTED?


     You may vote either "for" all nominees to the Board of Directors or you may
"withhold authority" (abstain) to vote for any nominee you specify. You may vote
"for," "against," or "abstain" on the proposed share increase for the 1997
Equity Incentive Plan, the proposed amendment to the Company's Certificate of
Incorporation to increase the number of authorized shares of common stock and
the ratification of the independent auditors. Shares represented by proxies that
reflect abstentions or "broker non-votes" (i.e. shares held by a broker or
nominee which are represented at the meeting, but with respect to which such
broker or nominee is not empowered to vote on a particular proposal) will be
counted as shares that are present and entitled to vote for purposes of
determining the presence of a quorum and will have the same effect as a vote
against a proposal. A vote "for" any nominee or any proposal is the same as a
"yes" vote.



WILL MY SHARES BE VOTED IF I DO NOT SIGN AND RETURN MY PROXY CARD OR MY VOTING
INSTRUCTION CARD?



     If you are a stockholder of record and you do not sign and return your
proxy card, your shares will not be voted. If you are the beneficial owner and
you do not sign and return your voting instruction card, the stockholder of
record may either vote your shares on routine matters or "non-vote" your shares.
These non-voted shares, known as broker non-votes, are counted for purposes of
establishing a quorum to conduct business at the meeting, but are not counted
for purposes of determining the outcome of any matter voted on.


HOW DO I VOTE?


     The simplest way for both stockholders of record and beneficial owners to
vote is to sign and date the enclosed proxy card or voting instruction card and
return it in the enclosed postage-prepaid envelope. The shares represented by a
signed and dated proxy card or a properly completed voting instruction card will
be voted in accordance with the directions given. If you return a signed and
dated proxy card or voting instruction card without marking any selections, your
shares will be voted in favor of the four proposals, except in the case of a
"broker non-vote". If you are a stockholder of record and return your proxy
card, you may revoke your proxy any time before the meeting by 1) notifying the
Company's Secretary (William J. Newell) in writing, or 2) submitting to the
Company a proxy with a later date. Of course, you also may revoke your proxy by
attending the annual meeting and voting in person. However, your attendance at
the meeting will not constitute a revocation of your proxy unless you actually
vote at the meeting. If you are a beneficial owner, you can vote your shares
through your broker, in person at the annual meeting or by using the enclosed
voting instruction card.


WHO WILL COUNT THE VOTE?

     Representatives of CompuShare Investor Services, Inc., Axys' transfer
agent, will perform the initial vote count and will assist David E. Riggs, Axys'
Senior Vice President and Chief Financial Officer, who will serve as the
inspector of the election and report the final vote count.

WHAT DOES IT MEAN IF I GET MORE THAN ONE PROXY CARD?

     It may indicate that your shares are registered under more than one name or
that you have multiple accounts in which you hold your shares. Please complete,
sign and return all proxy cards to ensure that your vote is counted.

                                        3
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WHAT IS A QUORUM AND WHAT CONSTITUTES A QUORUM?

     For the annual meeting to begin, a quorum of stockholders must attend the
meeting, either in person or by proxy. A majority of the outstanding shares as
of the record date -- present at the annual meeting or represented by valid
proxies -- constitutes a quorum for the annual meeting. If you submit a valid
proxy card or attend the annual meeting, you will be considered part of the
quorum.

     However, if there is no quorum, a majority of the shares present and
represented at the annual meeting may adjourn the annual meeting to another
date, time and place.


     At the record date (April 9, 2001), there were approximately 510
stockholders of record. There were 37,511,734 shares of Axys common stock
outstanding and entitled to vote at the annual meeting.


HOW CAN I FIND OUT THE RESULTS OF THE VOTING AT THE ANNUAL MEETING?

     The Company will announce preliminary voting results at the annual meeting
and publish final results in its quarterly report on Form 10-Q for the second
quarter of 2001.

WHEN ARE STOCKHOLDER PROPOSALS DUE FOR NEXT YEAR'S ANNUAL MEETING IN 2002?


     To be eligible for inclusion in next year's proxy statement and proxy,
stockholder proposals must be submitted in writing by December 19, 2001, to
William J. Newell, Secretary, Axys Pharmaceuticals, Inc., 180 Kimball Way, South
San Francisco, California 94080 (or e-mail to bill_newell@axyspharm.com). As
stated in the Company's bylaws, stockholder proposals for next year's annual
meeting or nominations for director may be properly raised at next year's annual
meeting even if they are not to be included in next year's proxy statement and
proxy. However, to do so, they must be submitted to the Company's Secretary
(William J. Newell) at the above listed address between February 13, 2002 and
March 15, 2002 and must confirm to the requirements of the Company's bylaws.




                                        4
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                           PROPOSALS TO BE VOTED UPON

                            1. ELECTION OF DIRECTORS
                             (ITEM 1 ON PROXY CARD)


     The Board of Directors currently consists of seven directors of Axys who
are elected annually. All nominees listed below are current directors of Axys.
The Board recommends a vote FOR each of these nominees. The term of office for
directors elected at the 2001 annual meeting will expire upon the election of
the Board at the 2002 annual meeting. See the section entitled "Nominees for
Directors" below for biographical information on the Board nominees.


  2. APPROVAL OF A 1,500,000 SHARE INCREASE IN THE NUMBER OF SHARES OF COMMON
                                STOCK AUTHORIZED
              FOR ISSUANCE UNDER AXYS' 1997 EQUITY INCENTIVE PLAN.
                             (ITEM 2 ON PROXY CARD)


     Axys is requesting approval for 1,500,000 additional shares of the
Company's common stock to become available for issuance under its 1997 Equity
Incentive Plan increasing the number of shares available for issuance thereunder
from 4,000,000 to 5,500,000. The Board recommends a vote FOR this proposal. See
the section entitled "General Description of the 1997 Equity Incentive Plan"
below for a summary of the 1997 Equity Incentive Plan.


  3. APPROVAL OF AN AMENDMENT TO THE COMPANY'S CERTIFICATE OF INCORPORATION TO
                             INCREASE THE NUMBER OF
             AUTHORIZED SHARES OF COMMON STOCK BY 50,000,000 SHARES
                             (ITEM 3 ON PROXY CARD)


     Axys is requesting approval of an amendment to the Company's Restated
Certificate of Incorporation to increase the number of authorized shares of the
Company's common stock by 50,000,000 shares increasing the number of authorized
shares of common stock from 50,000,000 to 100,000,000. The Board recommends a
vote FOR this proposal. See the section entitled "Amendment to Axys' Certificate
of Incorporation" below for a description of this amendment to Axys'
Certification of Incorporation.


             4. RATIFICATION OF APPOINTMENT OF INDEPENDENT AUDITORS
                             (ITEM 4 ON PROXY CARD)

     Stockholders will vote on the ratification of Ernst & Young LLP, certified
public accountants, to audit Axys' books, records and accounts for the year
ending December 31, 2001. Both the Audit Committee and the Board recommend a
vote FOR the adoption of this proposal. Representatives of Ernst & Young LLP
will be present at the annual meeting to answer appropriate questions. If the
stockholders do not ratify this appointment, the Board will reconsider the
selection of the auditors. The Board recommends a vote FOR this ratification.

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                             NOMINEES FOR DIRECTORS

     The information set forth below as to each nominee for director has been
furnished to us by the respective nominees:

JOHN P. WALKER -- DIRECTOR SINCE 1993


     Mr. Walker, 52, has been the Chairman of Axys since 1998 and was Chief
Executive Officer from 1993 to 2000. Prior to joining Axys, Mr. Walker was the
Chairman and Chief Executive Officer of Vitaphore Corporation, a medical device
company that was sold to Union Carbide in 1990. Prior to that, he spent 15 years
as an executive with American Hospital Supply Corporation, most recently serving
as President of the Hospital Company. Mr. Walker also serves as Chairman of
Microcide Corporation and is on the Boards of Directors of Geron Corporation,
Discovery Partners International, Inc. and the Biotechnology Industry
Organization.


ANN M. ARVIN, M.D. -- DIRECTOR SINCE 1997

     Dr. Arvin, 55, is the Lucile Salter Packard Professor of Pediatrics and
Microbiology/Immunology Stanford University School of Medicine, Stanford,
California. Dr. Arvin is also Chief of the Infectious Disease Service of the
Lucile Salter Packard Children's Hospital at Stanford and Associate Dean of
Research Stanford University. Since 1978, Dr. Arvin has taught at the Stanford
University School of Medicine. She is also currently a member of the Scientific
Advisory Board of Aviron.

VAUGHN M. KAILIAN -- DIRECTOR SINCE 1995

     Mr. Kailian, 56, is President, Chief Executive Officer and a director of
COR Therapeutics, Inc., a biotechnology company. He has served in these
capacities since March 1990. Mr. Kailian also serves as a director of Amylin
Pharmaceuticals, Inc.

PAUL J. HASTINGS -- DIRECTOR SINCE 2000


     Paul Hastings, 41, is the President and Chief Executive Officer of Axys and
a member of the Axys Board of Directors. Mr. Hastings became a director in
December 2000 and was appointed as Axys' President and Chief Executive Officer
in January 2001. Mr. Hastings joined the Company from Chiron Corporation of
Emeryville, California, where he was President of Chiron Bio-Pharmaceuticals
from 1999 to 2000. Before Chiron, from 1998 to 1999, Mr. Hastings served as the
President and Chief Executive Officer of LXR Biotechnology, a company focused on
the role of apoptosis in cardiovascular disease and oncology. From 1994 to 1998,
Mr. Hastings held a series of management positions at Genzyme Corporation of
Cambridge, Massachusetts, the last of which was President of Genzyme
Therapeutics worldwide. From 1989 to 1994, Mr. Hastings was at Synergen, in
Boulder, Colorado, as Vice President of Marketing and Sales and General Manager,
Synergen Europe, and from 1984 to 1989, was with Hoffmann-La Roche, Nutley, New
Jersey in marketing and sales management positions.


IRWIN LERNER -- DIRECTOR SINCE 1998


     Mr. Lerner, 70, was Chairman of the Board of Sequana Therapeutics, Inc.,
from May 1995 until January 1998 when Axys acquired Sequana. Mr. Lerner served
as Chairman of the Board of the Executive Committee of Hoffmann-La Roche Inc., a
pharmaceutical and health care company, from January 1993 until his retirement
in September 1993. He also served as its President and Chief Executive Officer
from 1980 through 1992. Mr. Lerner also serves on the Boards of Directors of
Public Service Enterprise Group, Humana Inc., Covance Inc., V.I. Technologies,
Inc., several private companies and is Chairman of the Board of Medarex Inc. He
is currently a Distinguished Executive-in-Residence at Rutgers University
Graduate School of Management.


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   11

ALAN C. MENDELSON, J.D. -- DIRECTOR SINCE 1999


     Mr. Mendelson, 53, is a senior partner of Latham & Watkins, a private law
firm, and has been with the firm since May of 2000. Previously, Mr. Mendelson
was with Cooley Godward LLP, a private law firm, for 27 years and served as the
managing partner of its Palo Alto office from May 1990 to March 1995 and
November 1996 to October 1997. Mr. Mendelson served as Secretary of Axys from
July 1993 through August 1998, with the exception of several months in 1994. Mr.
Mendelson formerly served as a director of the Company from May 1997 to January
1998, when he resigned in connection with the Company's acquisition of Sequana.
Mr. Mendelson also served as Acting General Counsel of Cadence Design Systems,
Inc., an electronic design automation software company, from November 1995 to
June 1996. Mr. Mendelson is currently a director of Aviron, USSearch.com, Inc.
and Valentis Inc. He has served as the President of the Board of Directors of
the National Kidney Foundation of Northern California and is a member of the
Major Gifts Council for the Lucile Packard Foundation for Children's Health.


J. LEIGHTON READ, M.D. -- DIRECTOR SINCE 1998

     Dr. Read, 50, is a private investor. He is the founder and was the Chairman
of the Board of Aviron, a biopharmaceutical company, from 1992 until 2000. From
1991 to 1993, he was a partner in Interhealth Limited, an investment
partnership. In 1987, Dr. Read co-founded Affymax N.V. with Dr. Alejandro
Zaffaroni, serving initially as its Executive Vice President and Chief Operating
Officer and later as President of the Pharma Division of Affymax and as a
Managing Director of the parent company of Affymax. Dr. Read has served on the
boards of a number of private biotechnology companies and currently serves on
the boards of Aviron and CV Therapeutics, Inc.


     The Company is not aware of any family relationships between any of the
foregoing nominees for director or between any nominee and any executive
officer. The Certificate of Incorporation and Bylaws of the Company contain
provisions eliminating or limiting the personal liability of directors for
violations of a director's fiduciary duty to the extent permitted by the General
Corporation Law of the State of Delaware. In addition, the Company has entered
into indemnification agreements with each of its directors.


                                BOARD COMMITTEES


     During the fiscal year ended December 31, 2000, the Board of Directors met
five times and acted once by written consent. Each incumbent director attended
at least 75% of the aggregate of the total number of meetings of the Board of
Directors held during such period (and for which he or she served as a
director). We have an Audit Committee, a Compensation Committee and an Option
Committee.



     Audit Committee. The Audit Committee, which was comprised of Dr. Arvin, Mr.
Lerner and Dr. Donald Kennedy (until Dr. Kennedy resigned from the Board of
Directors and the Audit Committee in December 2000) met two times in 2000. Mr.
Lerner serves as the Chairman of the Audit Committee. On February 1, 2001, Mr.
Mendelson was appointed to replace Dr. Kennedy on the Audit Committee. In
accordance with its written charter which has been approved by the Board, a copy
of which is attached to this proxy statement as Appendix A, the Audit
Committee's responsibilities include: (1) recommending the selection of our
independent public auditors to the Board of Directors, (2) consulting with the
independent auditors with regard to the plan and scope of audit, (3) reviewing,
in consultation with the independent auditors, their report of audit or proposed
report of audit, and the accompanying management letter, if any, and (4)
consulting with the independent auditors and management with regard to the
adequacy of internal controls.



     Compensation Committee. Mr. Kailian and Dr. Read serve on the Compensation
Committee, which met two times in 2000. The Compensation Committee reviews and
approves the compensation of Axys' executive officers, is responsible for the
Company's employee benefit plans and programs, including their establishment,
modification and administration, and performs other related functions upon
request of the Board.


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   12

     Option Committee. Mr. Walker was the only member of the Option Committee
during 2000 which reviews and administers the Company's 1997 Equity Incentive
Plan and the 1997 Non-Officer Equity Incentive Plan for stock option grants to
non-executive officer employees. The Option Committee has the authority to
approve the price and terms of these options, within the limits set by the
Board.

     The Board does not have a Nominating Committee or a committee serving a
similar function. Nominations of directors are considered by the Board as a
whole.

                     COMPENSATION OF NON-EMPLOYEE DIRECTORS


     Compensation. In 2000, compensation for non-employee directors was $15,000
per year, plus reimbursement of expenses. In addition, Mr. Lerner received an
additional $30,000 as compensation for consulting services he provided to Axys
during 2000. Mr. Walker, who was an employee of the Company during 2000,
received no compensation for his services during 2000 as a director. Mr.
Hastings was appointed to the board in December 2000 and became an employee
January 2001. Mr. Hastings received no compensation for his services in 2000.



     Stock Options. According to the Company's Non-Employee Directors' Stock
Option Plan established in 1994, non-employee directors of Axys receive annual
automatic stock option grants. The terms of the Non-Employee Directors' Stock
Option Plan provide that each non-employee elected for the first time to Axys'
Board will be granted an option to purchase 30,000 shares of common stock upon
the date of his or her initial election or appointment. On the date of each
annual meeting, each non-employee Board member who has served for at least three
months, and is re-elected to the Board, is automatically granted a non-qualified
stock option to purchase 5,000 shares of common stock of the Company. No other
options may be granted at any time under this plan. The exercise price of the
options that are granted is 100% of the fair market value of the common stock on
the date of the option grant. Options granted under the plan generally vest at a
rate of 25% per year for four years. The term of the options is ten years. In
the event of a change-in-control of Axys, such as a merger with or into another
corporation or a consolidation, the vesting of these options will accelerate and
the options expire if not exercised prior to the change-in-control. As of
February 28, 2001, none of the options granted under the plan had been
exercised. Following their election at the 2000 annual meeting, each of Dr.
Arvin, Dr. Kennedy, Dr. Read, Mr. Mendelson, Mr. Kailian, and Mr. Lerner
received options to acquire 5,000 shares of common stock at an exercise price of
$4.063 per share.



     Stock Grants. In December 2000, the Board resolved to make grants of common
stock to Mr. Kailian, Mr. Lerner and Mr. Mendelson in the amounts of 2,500
shares, 1,500 shares and 2,500 shares, respectively. These stock grants were
made for service on the Board's Chief Executive Officer Search Committee by Mr.
Kailian, Mr. Lerner and Mr. Mendelson following Mr. Walker's announcement of his
intent to resign as the Chief Executive Officer of Axys upon the appointment of
his successor.


                                        8
   13

         STOCK OWNERSHIP OF BENEFICIAL OWNERS, DIRECTORS AND MANAGEMENT

     The following table sets forth, as of February 28, 2001, the amount and
percentage of the outstanding shares of our common stock which, according to the
information supplied to us, are beneficially owned by (i) each person or entity
who, to the knowledge of the Company, is the beneficial owner of more than 5% of
the outstanding common stock, (ii) each person who is currently a director of
the Company (each of whom is also a nominee), (iii) each Named Executive Officer
(as defined in the section entitled "Compensation of Executive Officers" on page
11 hereof) and (iv) all current directors and executive officers of the Company
as a group. Except to the extent indicated in the footnotes to the following
table, the person or entity listed has sole voting or dispositive power with
respect to the shares which are deemed beneficially owned by such person or
entity.


     The information in the table is based on reports that have been filed with
the Securities and Exchange Commission (the "SEC") pursuant to the Securities
Exchange Act of 1934, as amended (the "Exchange Act"), and information furnished
to the Company by certain holders of common stock. As of February 28, 2001,
there were 37,389,307 shares of common stock outstanding. In accordance with
regulations promulgated by the SEC, the table reflects for each beneficial owner
the exercise of warrants or options or the conversion of convertible securities
(exercisable or convertible within 60 days after February 28, 2001) owned by
such beneficial owner, but, in determining the percentage ownership and general
voting power of such person, does not assume the exercise of warrants or options
or the conversion of securities owned by any other person.





                                                            OPTIONS/        TOTAL         PERCENT OF
                                                            WARRANTS     OUTSTANDING      OUTSTANDING
                                            OUTSTANDING    EXERCISABLE   COMMON STOCK      SHARES OF
           NAME AND ADDRESS OF                COMMON         WITHIN      BENEFICIALLY       COMMON
             BENEFICIAL OWNER                  STOCK         60 DAYS        OWNED            STOCK
           -------------------              -----------    -----------   ------------     -----------
                                                                            
DIRECTORS/NOMINEES AND NAMED EXECUTIVE
  OFFICERS
Ann M. Arvin, M.D. .......................           0         26,250        26,250             *
Paul J. Hastings(1).......................           0              0             0             *
Daniel F. Hoth, M.D. .....................      12,940(2)      89,375       102,315             *
Vaughn M. Kailian.........................       2,500         29,074        31,574             *
Irwin Lerner..............................      69,225(3)      40,833       110,058             *
Alan C. Mendelson.........................       5,329(4)      24,896        30,225             *
William J. Newell, J.D. ..................      26,124(5)     110,209       136,333             *
J. Leighton Read, M.D. ...................       3,000         26,250        29,250             *
Michael C. Venuti, Ph.D. .................      26,632(6)     177,293       203,925             *
John P. Walker............................     248,563(7)     385,958       634,521           1.7%
All directors and executive officers as a
  group (12 persons)(8)...................     394,313        942,637     1,336,884           3.5%
5% BENEFICIAL HOLDERS
Wellington Management Company, LLP(9).....   3,385,400              0     3,835,400          10.3%
  75 State Street
  Boston, Massachusetts 02109
Bay City Capital(10)......................           0      2,482,758     2,482,758           6.2%
  750 Battery Street
  San Francisco, CA 94111



- ---------------
  *  Less than one percent.


 (1) Mr. Hastings became a Director of Axys in December 2000 and the President
     and Chief Executive Officer of Axys in January 2001.



 (2) Includes 10,500 shares acquired pursuant to a restricted stock grant.



 (3) Includes 1,350 shares beneficially owned by Mr. Lerner's wife and 1,500
     shares acquired as consideration for services provided on Axys' Chief
     Executive Officer Search Committee.


                                        9
   14


 (4) Includes 2,500 shares acquired as consideration for services provided on
     Axys' Chief Executive Officer Search Committee.



 (5) Includes 12,250 shares acquired pursuant to a restricted stock grant.



 (6) Includes 15,500 shares acquired pursuant to a restricted stock grant.



 (7) Includes 26,123 shares held in the Walker Living Trust and 8,574 shares
     beneficially owned by Mr. Walker's wife as trustee of educational trusts
     for his children.



 (8)Includes David E. Riggs who became the Senior Vice President and Chief
    Financial Officer of Axys in September 2000 and Douglas H. Altschuler who
    became the Vice President and General Counsel of Axys in December 2000.



 (9)Information regarding the ownership of common stock by Wellington Management
    Company, LLP ("Wellington") was obtained from a Schedule 13G, dated February
    28, 2001. Wellington reports shared dispositive power for all 3,835,400
    shares and shared voting power over 3,029,100 shares.



(10)Subsequent to February 28, 2001, Bay City Capital, acting through two of its
    funds, exercised its options to acquire 2,482,758 shares of Axys common
    stock.




                                        10
   15

                       COMPENSATION OF EXECUTIVE OFFICERS

     The following table sets forth certain information regarding the annual and
long-term compensation for services in all capacities to the Company for the
fiscal years ended December 31, 1998, December 31, 1999 and December 31, 2000 of
those persons who were either (i) the chief executive officer of the Company
during the fiscal year ended December 31, 2000, (ii) up to four most highly
compensated executive officers of the Company whose annual salary and bonuses
exceeded $100,000 who were serving as an executive officer at December 31, 2000
or (iii) up to two other executive officers who would have qualified under
sections (i) or (ii) of this paragraph but for the fact that the individual was
not serving as an executive officer of the Company at the end of the 2000 fiscal
year (collectively, the "Named Executive Officers").

                           SUMMARY COMPENSATION TABLE




                                                                             LONG-TERM COMPENSATION
                                                                                     AWARDS
                                                                          ----------------------------
                                        ANNUAL COMPENSATION               RESTRICTED      SECURITIES         ALL OTHER
                               --------------------------------------       STOCK         UNDERLYING           ANNUAL
 NAME AND PRINCIPAL POSITION   YEAR   SALARY($)   BONUS($)   OTHER($)     AWARDS($)      OPTIONS(#)(1)   COMPENSATION($)(2)
 ---------------------------   ----   ---------   --------   --------     ----------     -------------   ------------------
                                                                                    
John P. Walker(3)............  2000    425,015    138,125    909,540(4)         --       268,322(5)            19,927(6)
  Chairman and Chief           1999    410,000         --    247,250(7)         --           85,000             7,979
  Executive Officer            1998    390,000    135,000    261,252(7)         --       435,000(8)             6,150
Michael C. Venuti, Ph.D. ....  2000    262,510     57,093         --            --       246,823(9)               911(10)
  Senior Vice President,       1999    250,000         --         --      112,375(11)       103,000             1,188
  Research and Preclinical     1998    235,000     47,000         --            --       197,000(8)               696
  Development, Chief
  Technical Officer
Daniel F. Hoth, M.D.(12).....  2000    288,503     62,748         --            --       209,323(13)            6,335(14)
  Senior Vice President,       1999    151,666         --         --      76,125(11)        150,000             5,327
  Clinical Development,
  Chief Medical Officer
William J. Newell,
  J.D.(15)...................  2000    255,000     61,200         --            --       211,823(16)              414(17)
  Senior Vice President,       1999    238,417         --         --      88,812(11)        115,000             5,703
  Corporate and Business       1998    102,404     22,559         --            --           75,000                --
  Development, General
  Counsel & Secretary



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

 (1)Includes options to acquire the Company's common stock and options to
    acquire capital stock of certain of the Company's affiliated companies
    pursuant to the 1999 Key Personnel Stock Option Plan.



 (2) Consists of Company matching contributions under the Company's 401(k)
     retirement plan and life insurance premiums.



 (3)Mr. Walker was Chief Executive Officer of Axys until December 31, 2000. Mr.
    Paul J. Hastings became the President and Chief Executive Officer of Axys on
    January 2, 2001. See the section entitled "-- Management Agreements" below
    for a description of Mr. Hastings employment agreement.



 (4) Consists of the forgiveness of principal and interest due on one promissory
     note in the aggregate amount of $685,540 and a tax gross-up in the
     aggregate amount of $224,000 pursuant to Mr. Walker's amended and restated
     employment agreement. See "Compensation of Executive Officers."



 (5) Includes options to acquire 100,000 shares of the Company's common stock
     and the following options to acquire stock in Axys' affiliated companies
     granted to Mr. Walker pursuant to the 1999 Key Personnel Stock Option Plan:
     (i) options to acquire 50,000 shares of preferred stock of Akkadix
     Corporation at an exercise price of $3.33 per share, (ii) options to
     acquire 114,800 shares of series A preferred stock of PPGx, Inc. at an
     exercise price of $6.11 per share (following the acquisition of PPGx. Inc.
     by DNA Sciences, Inc. in December 2000 these options became fully vested
     options to acquire 33,947 shares of series D preferred stock of DNA
     Sciences, Inc. at an exercise price of $20.66 per share, the options to
     acquire preferred stock of DNA Sciences, Inc. are included above) and (iii)
     options to acquire 112,500 shares of common stock of Axys Advanced
     Technologies, Inc. at an exercise price of $1.00 (following the acquisition
     of Axys Advanced Technologies, Inc. by Discovery Partners International,
     Inc. in April 2000 these options became fully vested options to acquire
     84,375 shares of common stock of Discovery Partners International, Inc. at
     an exercise price of $1.33 per share, the options to acquire common stock
     of Discovery Partners International, Inc. are included above).


                                        11
   16


 (6)In 2000, Axys paid a total of $14,677 in life insurance premiums for Mr.
    Walker and $5,250 in matching contributions to Mr. Walker's 401(k)
    retirement plan.



 (7) Consists of the forgiveness of principal and interest due and an interest
     rate reduction under one promissory note.



 (8) Includes stock options which were canceled and regranted in connection with
     the Company's stock option repricing in 1998, as follows: Mr. Walker,
     375,000 shares; and Dr. Venuti, 147,000 shares.



 (9) Includes options to acquire 110,000 shares of the Company's common stock
     and the following options to acquire stock in Axys' affiliated companies
     granted to Dr. Venuti pursuant to the 1999 Key Personnel Stock Option Plan:
     (i) options to acquire 40,000 shares of preferred stock of Akkadix
     Corporation at an exercise price of $3.33 per share, (ii) options to
     acquire 73,800 shares of series A preferred stock of PPGx, Inc. at an
     exercise price of $6.11 per share (following the acquisition of PPGx. Inc.
     by DNA Sciences, Inc. in December 2000 these options became fully vested
     options to acquire 21,823 shares of series D preferred stock of DNA
     Sciences, Inc. at an exercise price of $20.66 per share, the options to
     acquire preferred stock of DNA Sciences, Inc. are included above) and (iii)
     options to acquire 100,000 shares of common stock of Axys Advanced
     Technologies, Inc. at an exercise price of $1.00 (following the acquisition
     of Axys Advanced Technologies, Inc. by Discovery Partners International,
     Inc. in April 2000 these options became fully vested options to acquire
     75,000 shares of common stock of Discovery Partners International, Inc. at
     an exercise price of $1.33 per share, the options to acquire common stock
     of Discovery Partners International, Inc. are included above).



(10)In 2000, Axys paid a total of $911 in life insurance premiums for Dr.
    Venuti.



(11) Fair market value of restricted stock bonus at the time of grant was $7.25
     per share of common stock. These officers voluntarily agreed to receive
     restricted shares, which may not be sold for one year after grant except in
     limited circumstances, in lieu of a cash bonus that they otherwise would
     have been entitled to receive. Dr. Hoth received 10,500 shares, Mr. Newell
     received 12,250 shares and Dr. Venuti received 15,500 shares.



(12) Dr. Hoth joined the Company in June 1999.



(13) Includes options to acquire 110,000 shares of the Company's common stock
     and the following options to acquire stock in Axys' affiliated companies
     granted to Dr. Hoth pursuant to the 1999 Key Personnel Stock Option Plan:
     (i) options to acquire 40,000 shares of preferred stock of Akkadix
     Corporation at an exercise price of $3.33 per share, (ii) options to
     acquire 73,800 shares of series A preferred stock of PPGx, Inc. at an
     exercise price of $6.11 per share (following the acquisition of PPGx. Inc.
     by DNA Sciences, Inc. in December 2000 these options became fully vested
     options to acquire 21,823 shares of series D preferred stock of DNA
     Sciences, Inc. at an exercise price of $20.66 per share, the options to
     acquire preferred stock of DNA Sciences, Inc. are included above) and (iii)
     options to acquire 50,000 shares of common stock of Axys Advanced
     Technologies, Inc. at an exercise price of $1.00 (following the acquisition
     of Axys Advanced Technologies, Inc. by Discovery Partners International,
     Inc. in April 2000 these options became fully vested options to acquire
     37,500 shares of common stock of Discovery Partners International, Inc. at
     an exercise price of $1.33 per share, the options to acquire common stock
     of Discovery Partners International, Inc. are included above).



(14)In 2000, Axys paid a total of $1,091 in life insurance premiums for Dr. Hoth
    and $5,250 in matching contributions to Dr. Hoth's 401(k) retirement plan.



(15) Mr. Newell joined the Company in July 1998.



(16) Includes options to acquire 75,000 shares of the Company's common stock and
     the following options to acquire stock in Axys' affiliated companies
     granted to Mr. Newell pursuant to the 1999 Key Personnel Stock Option Plan:
     (i) options to acquire 40,000 shares of preferred stock of Akkadix
     Corporation at an exercise price of $3.33 per share, (ii) options to
     acquire 73,800 shares of series A preferred stock of PPGx, Inc. at an
     exercise price of $6.11 per share (following the acquisition of PPGx. Inc.
     by DNA Sciences, Inc. in December 2000 these options became fully vested
     options to acquire 21,823 shares of series D preferred stock of DNA
     Sciences, Inc. at an exercise price of $20.66 per share, the options to
     acquire preferred stock of DNA Sciences, Inc. are included above) and (iii)
     options to acquire 100,000


                                        12
   17


     shares of common stock of Axys Advanced Technologies, Inc. at an exercise
     price of $1.00 (following the acquisition of Axys Advanced Technologies,
     Inc. by Discovery Partners International, Inc. in April 2000 these options
     became fully vested options to acquire 75,000 shares of common stock of
     Discovery Partners International, Inc. at an exercise price of $1.33 per
     share, the options to acquire common stock of Discovery Partners
     International, Inc. are included above).



(17)In 2000, Axys paid a total of $414 in life insurance premiums for Mr.
    Newell.



     The following table sets forth certain information with respect to grants
of stock options during fiscal 2000 to the Named Executive Officers pursuant to
the Company's 1997 Equity Incentive Plan, as amended and the 1999 Key Personnel
Option Plan.


                       OPTION GRANTS IN LAST FISCAL YEAR




                                                                                        POTENTIAL
                                          PERCENTAGE                               REALIZABLE VALUE AT
                                           OF TOTAL                                  ASSUMED ANNUAL
                             NUMBER OF     OPTIONS                                RATES OF STOCK PRICE
                             SECURITIES   GRANTED TO                                  APPRECIATION
                             UNDERLYING   EMPLOYEES     PER SHARE                  FOR OPTION TERM(1)
                              OPTIONS     IN FISCAL     EXERCISE     EXPIRATION   ---------------------
           NAME               GRANTED      YEAR(2)     PRICE(3)(4)      DATE         5%         10%
           ----              ----------   ----------   -----------   ----------   --------   ----------
                                                                           
John P. Walker.............   100,000(5)      4.5%       $ 7.25       01/28/10    $455,949   $1,155,463
                               50,000(7)     20.0          3.33       12/14/10     104,711      265,358
                               84,375(8)     22.5          1.33        2/11/10      70,574      178,848
                               33,947(9)     28.0         20.66       12/14/10     441,072    1,117,763
Michael C. Venuti,
  Ph.D. ...................    50,000(5)      2.3          7.25       01/28/10     227,974      577,732
                               60,000(5)      2.7          4.875      12/14/10     183,952      466,170
                               40,000(7)     16.0          3.33       12/14/10      83,769      212,286
                               75,000(8)     20.0          1.33        2/11/10      62,732      158,976
                               21,823(9)     18.0         20.66       12/14/10     283,545      718,560
Daniel F. Hoth, M.D. ......    50,000(6)      2.3          7.25       01/28/10     227,974      577,732
                               60,000(6)      2.7          4.875      12/14/10     183,952      466,170
                               40,000(7)     16.0          3.33       12/14/10      83,769      212,286
                               37,500(8)     10.0          1.33        2/11/10      31,366       79,488
                               21,823(9)     18.0         20.66       12/14/10     283,545      718,560
William J. Newell, J.D. ...    25,000(5)      1.1          7.25       01/28/10     113,987      288,866
                               50,000(5)      2.3          4.875      12/14/10     153,293      388,475
                               40,000(7)     16.0          3.33       12/14/10      83,769      212,286
                               75,000(8)     20.0          1.33        2/11/10      62,732      158,976
                               21,823(9)     18.0         20.66       12/14/10     283,545      718,560



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

(1) Potential realizable value is based on the assumption that the common stock
    of the Company or the capital stock of the affiliated companies appreciates
    at the annual rate shown (compounded annually) from the date of grant until
    the expiration of the ten-year option term. The 5% and 10% assumed rates of
    appreciation are mandated by the rules of the Securities and Exchange
    Commission and do not reflect the Company's estimate or projection of the
    future stock prices.



(2)For options to acquire shares of the Company's common stock, the percentage
   refers to the percentage of the total options to acquire the Company's common
   stock granted to employees in 2000. For options to acquire shares of capital
   stock of certain of the Company's affiliated companies, the percentage refers
   to the percentage of the total options to acquire the capital stock of each
   respective affiliated company granted to employees in 2000.



(3) Options to acquire shares of the Company's common stock were granted at a
    price equal to the fair market value of the Company's common stock on the
    date of grant. Fair market value is determined by reference to the closing
    sale price of the common stock on the Nasdaq National Market.



(4)Options to acquire capital stock of certain of the Company's affiliated
   companies at a price equal to the fair market value of capital stock of the
   respective affiliated companies on the date of grant. Fair market value was
   determined by the Board at the time of grant.


                                        13
   18


(5) Options to acquire shares of the Company's common stock which vest in equal
    monthly installments over four years from the date of grant.



(6) Options to acquire shares of the Company's common stock. One-eighth of the
    shares vest after six months, the remaining shares vest in equal monthly
    installments over the following three and one half years.



(7)Options to acquire shares of preferred stock of Akkadix Corporation which
   vest in equal monthly installments over four years from the date of grant.



(8)Fully vested options to acquire shares of common stock of Discovery Partners
   International, Inc. At the time of grant, these were options to acquire
   shares of common stock of the Company's subsidiary Axys Advanced
   Technologies, Inc. Following the acquisition of Axys Advanced Technologies,
   Inc., these became fully vested options to acquire shares of common stock of
   Discovery Partners International, Inc.



(9)Fully vested options to acquire shares of preferred stock of DNA Sciences,
   Inc. At the time of grant, these were options to acquire shares of preferred
   stock of the Company's subsidiary, PPGx, Inc. Following the acquisition of
   PPGx, Inc. by DNA Sciences, Inc., these became fully vested options to
   acquire shares of preferred stock of DNA Sciences, Inc.


     The following table sets forth certain information with respect to options
exercised during fiscal 2000 and exercisable and unexercisable options held by
the Named Executive Officers as of December 31, 2000.

   AGGREGATED OPTION EXERCISES IN LAST FISCAL YEAR AND YEAR-END OPTION VALUE




                                                         NUMBER OF SECURITIES           VALUE OF UNEXERCISED
                                                        UNDERLYING UNEXERCISED              IN-THE-MONEY
                                                              OPTIONS AT                     OPTIONS AT
                              SHARES                        FISCAL YEAR END              FISCAL YEAR END(1)
                            ACQUIRED ON    VALUE     -----------------------------   ---------------------------
                             EXERCISE     REALIZED   EXERCISABLE     UNEXERCISABLE   EXERCISABLE   UNEXERCISABLE
                            -----------   --------   -----------     -------------   -----------   -------------
                                                                                 
John P. Walker............       --           --       348,409(2)       211,591       $218,042       $101,333
                                 --           --             0(3)        50,000             --       $      0
                                 --           --        84,375(4)             0       $910,828             --
                                 --           --        33,947(5)             0       $      0             --
Michael C. Venuti,
  Ph.D. ..................       --           --       162,748(2)       212,752       $117,432       $202,093
                                 --           --             0(3)        40,000             --       $      0
                                 --           --        75,000(4)             0       $809,625             --
                                 --           --        21,823(5)             0       $      0             --
Daniel F. Hoth, M.D. .....       --           --        77,333(2)       193,167       $115,988       $238,313
                                 --           --             0(3)        40,000             --       $      0
                                 --           --        37,500(4)             0       $404,813             --
                                 --           --        21,823(5)             0       $      0             --
William J. Newell,
  J.D. ...................       --           --        99,353(2)       177,897       $ 56,996       $175,155
                                 --           --             0(3)        40,000             --       $      0
                                 --           --        75,000(4)             0       $809,625             --
                                 --           --        21,823(5)             0       $      0             --



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

(1) Based on the fair market value of the securities underlying the option on
    December 31, 2000, minus the exercise price of the option, multiplied by the
    number of shares to which the option relates. The fair market value of the
    Company's common stock is based on the closing price of the common stock
    ($5.625) on December 29, 2000. The fair market value of the shares of
    preferred stock of Akkadix Corporation is based on the Company's
    determination of such fair market value ($3.33) on December 31, 2000. The
    fair market value of the common stock of Discovery Partners International,
    Inc. is based on the closing price of such common stock ($12.125) on
    December 29, 2000. The fair market value of the shares of preferred stock of
    DNA Sciences, Inc. is based on the Company's determination of such fair
    market value ($10.15) on December 31, 2000.



(2)Options to acquire shares of the Company's common stock.


                                        14
   19


(3)Options to acquire shares of preferred stock of Akkadix Corporation.



(4)Options to acquire shares of common stock of Discovery Partners
   International, Inc.



(5)Options to acquire shares of preferred stock of DNA Sciences, Inc.


MANAGEMENT AGREEMENTS


     Paul Hastings' Employment Agreement. Mr. Hastings became Axys' President
and Chief Executive Officer in January 2001. Mr. Hastings' employment agreement
with the Company (the "Hastings Employment Agreement") provides for an initial
annual base salary of $400,000, beginning in January 2001, and provides for an
annual bonus of up to fifty percent of Mr. Hastings' base salary, if Mr.
Hastings achieves certain target goals specified by the Board. In addition, the
Company loaned Mr. Hastings $300,000 pursuant to the terms of a promissory note
with an interest rate of 5.61%, per annum. This note is due and payable on
January 2, 2004, is full-recourse and is to be secured by shares of the
Company's common stock acquired by Mr. Hastings upon the exercise of any stock
options. If Mr. Hastings continues to provide his services to the Company
through January 2, 2004, the entire note will be forgiven by the Company. All
remaining principal and accrued interest under the promissory note will become
immediately due and payable upon Mr. Hastings' termination of service for any
reason other than Mr. Hastings' termination of employment for "Good Reason" or
Mr. Hastings' termination of employment without "Cause" or due to death or
disability.



     In connection with his employment agreement, Mr. Hastings was also granted
options to purchase 500,000 shares of common stock at the fair market value on
the date of grant which vest over a four year period. Mr. Hastings was also
granted non-statutory performance options to purchase an additional 100,000
shares of common stock which may vest over a four year period if certain
performance goals are met, or in the event such goals are not met, the entire
performance option will vest on the seventh anniversary of the grant date,
subject to Mr. Hastings continued employment at Axys. In addition, in the event
of certain terminations of employment, Mr. Hastings will continue for one year
to receive monthly payments in the amount equal to one-twelfth of the sum of his
base salary plus his target bonus amount and in the event of certain
terminations of employment in connection with a change in control of Axys, all
stock options held by Mr. Hastings that would have vested within twelve months
of the date of such termination, will immediately and automatically vest.



     William Newell's Employment Agreement. In 2001, the Company entered into an
amended and restated employment agreement with Mr. Newell to continue to serve
as Axys' senior vice president, corporate and business development. The
agreement provides, among other things, for an annual salary of $275,000 and
eligibility for a bonus in an amount up to 30% of his annual salary. In the
event of certain terminations of employment, Mr. Newell will receive a severance
payment equal to 100% of his annual base salary plus 100% of his target bonus,
and in the event of certain terminations of employment in connection with a
change in control of Axys, all of Mr. Newell's unvested stock options will
immediately and automatically vest.



     Michael Venuti's Employment Agreement. In 2001, the Company entered into an
amended and restated employment agreement with Dr. Venuti to continue to serve
as Axys' senior vice president, research and preclinical development and chief
technical officer. The agreement provides, among other things, for a starting
salary of $290,000 per year and eligibility for a bonus in an amount up to 30%
of his annual salary. In the event of certain terminations of employment, Dr.
Venuti will receive a severance payment equal to 100% of his annual base salary
and 100% of his target bonus amount, and in the event of certain terminations of
employment in connection with a change in control of Axys, all of Dr. Venuti's
unvested stock options will immediately and automatically become fully vested
and exercisable. In addition, in August 2000, the Company advanced Dr. Venuti
$300,000 in a note receivable which bears interest at 6.37% which is due
annually. Dr. Venuti's employment agreement provides that the note plus accrued
interest will be forgiven over five years, subject to Dr. Venuti's continued
employment with Axys. Dr. Venuti's employment agreement also provides that in
the event of certain terminations of employment, all remaining principal amounts
plus all accrued interest due under the promissory note would be immediately
forgiven.


     Daniel Hoth's Employment Agreement. In 2001, the Company entered into an
employment agreement with Dr. Hoth to continue to serve as Axys' Senior Vice
President, Clinical Development and Chief Medical

                                        15
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Officer. The agreement provides, among other things, for an annual salary of
$305,000 and eligibility for a bonus in an amount up to 30% of his annual
salary. In the event of certain terminations of employment, Dr. Hoth will
receive a severance payment equal to 100% of his base salary plus 100% of his
target bonus, and in the event of certain terminations of employment in
connection with a change in control of Axys, all of Dr. Hoth's unvested stock
options will immediately and automatically vest.



     John Walker's Agreement. Mr. Walker has an amended and restated employment
agreement with the Company to serve as non-executive chairman (the "Walker
Agreement"). The Walker Agreement provides for an annual salary of $212,500
beginning January 1, 2001 and the continuation of his split dollar life
insurance policy with a benefit payable to Mr. Walker of approximately $1.2
million. Mr. Walker had previously issued a promissory note to the Company of
which $400,000 remained unpaid and $94,611 in interest had accrued as of
December 14, 2000. Pursuant to the Walker Agreement, all outstanding principal
and interest due under this note was forgiven. In addition, Mr. Walker shall
also receive a tax gross-up payment of up to $160,000 to pay taxes due as a
result of the forgiveness of principal and interest due on the note.



     Under the Walker Agreement both parties have the right to terminate the
agreement at any time for any reason whatsoever, with or without "Cause" or
advance notice. If Mr. Walker's employment is terminated for any reason other
than death, disability, a voluntary termination not for "Good Reason", or a
termination for "Cause", then Mr. Walker shall receive a lump sum payment equal
to his remaining unpaid base salary and any unvested options held by Mr. Walker
shall immediately vest.



     Under the Walker Agreement, if during or for two years immediately
following the termination of the Walker Agreement, Mr. Walker, without prior
approval of the Company, directly or indirectly engages or prepares to engage in
any activities in competition with the Company, or accepts employment or
establishes a business relationship with a business engaged in or preparing to
engage in competition with the Company, then the 100,000 share stock option
grant originally made to Mr. Walker in October 1998 will, to the extent not
previously exercised or terminated pursuant to its terms, immediately terminate.


                                        16
   21

                      REPORT OF THE COMPENSATION COMMITTEE

WHAT IS THIS REPORT?

     The SEC requires that public companies disclose all procedures and
mechanisms that are used to establish officer compensation. This report explains
the criteria that the Company used to determine the compensation of its officers
in 2000.

WHO SERVES ON THE COMPENSATION COMMITTEE?

     The Compensation Committee consists of directors who are not employees of
the Company. During 2000, the Compensation Committee was composed of Mr. Kailian
and Dr. Read.

WHAT ARE THE COMPENSATION COMMITTEE'S RESPONSIBILITIES?

     The Compensation Committee is responsible for establishing and implementing
policies and programs to compensate the Company's executives. The Compensation
Committee met two times in 2000 to review and recommend compensation levels and
certain stock grants for all executive officers for 2000. The Compensation
Committee submits its recommendations to the entire Board for approval. The
Board adopted the Compensation Committee's recommendations without modification.

WHAT IS OUR COMPENSATION PHILOSOPHY?

     The primary objective of our executive compensation program is to attract,
retain and reward executive officers and other employees who contribute to the
long-term success of the Company and to motivate those individuals to enhance
long-term stockholder value. The Compensation Committee accomplishes this by:

          1. Establishing salaries competitive with those of leading
     biotechnology and pharmaceutical companies with which the Company competes
     for talent.

          2. Maintaining incentive opportunities designed to motivate and reward
     achievement of the Company's and each individual's goals. These incentives
     consist of cash bonuses and stock options, and are designed to bring the
     total compensation for key employees to competitive levels within the
     industry.

          3. Providing significant equity-based incentives for executives and
     other key employees to ensure that these individuals are motivated over the
     long term and respond to challenges and opportunities as owners and not
     just as employees.


     In light of the competitive environment in the Company's industry, the
Compensation Committee elected to have the Company enter into employment
agreements, or to amend existing employment agreements, with the Company's top
executives during the first quarter of 2001. The new employment agreements and
the amendments to the existing employment agreements were designed to provide
consistent compensation among the Company's top executives and to provide
competitive compensation packages in order to retain and motivate the Company's
top executives.


HOW IS EXECUTIVE BASE COMPENSATION DETERMINED?

     Salary. The base salary for all employees, including executive officers, is
based upon a review of an employee's salary level against the compensation of
employees in similar positions in other biotechnology and pharmaceutical
companies, in accordance with a published survey of the employee compensation of
companies of comparable size to the Company and in the same geographical region.
Base salaries are targeted at the third quartile for comparable positions in the
other companies. Salary adjustments for 2000 were based on each individual's
performance ranking. In January 2000, based on this information and on each
individual's performance in 1999, the Compensation Committee recommended 2000
base salary increases of 2.5% to 5.0% over 1999 base salaries for executive
officers, including the Chief Executive Officer. In establishing base salaries
for the Company's executive officers, the Compensation Committee carefully
reviewed the progress made in the programs headed by each executive officer in
2000, together with the achievements of each

                                        17
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executive officer and the departments reporting to such executive officer,
during 2000, and the dependence of the Company on these executive officers for
scientific and business development and executive leadership.

IS THERE A BONUS PROGRAM?


     Cash. A portion of the cash compensation is paid to the Company's executive
officers and other senior management personnel in the form of an annual bonus.
Bonus payments for 2000 were based 50% on the attainment of goals established
for the Company as a whole, and 50% on the attainment of goals established for
each executive officer, and were limited (except in cases of overachievement) to
a percentage of each executive officer's base salary, which ranged from 25% to
50% of an executive officer's respective base salary. General corporate goals in
2000 included, among other items, continued progress in the Company's
preclinical and clinical programs, expanding the Company's oncology pipeline,
creating value in the Company's affiliated businesses, achievement of financial
targets and increasing stockholder value. The Compensation Committee determined
after a review of the Company's achievement of scientific and business goals,
that a 65% achievement level was merited for each executive officer for the
component of the bonus calculations dependent on the Company's attainment of its
established goals for 2000. Based on its review of the degree of attainment of
Company and personal goals, the Compensation Committee recommended and the Board
approved individual bonuses ranging from 65% to 80% (applied pro rata where
appropriate) of the executive officer's respective targeted bonus amounts.



     Stock Options. One of the primary components of Axys' long-term incentive
program are its stock option plans. Through stock option grants that are based
on performance, executives receive significant equity incentives to build
long-term stockholder value. Stock option grants are also used to retain these
officers in light of the increasing demands placed on them due to the Company's
growth. The grants typically vest over a four-year period and are set at the
fair market value of Axys' common stock on the date of the grant. The
Compensation Committee does consider the number of options previously granted to
an executive in determining the size of a new grant. All Named Executive
Officers received stock option grants in January 2000. In December 2000,
additional stock options were granted to all the Named Executive Officers other
than Mr. Walker at levels reflecting, among other things, their contributions to
the achievement of the Company's and their personal goals in 2000 and the level
of stock grants recently awarded to them.



     In 1999, the Company adopted the 1999 Key Personnel Stock Option Plan (the
"Key Personnel Plan") which permits Axys to grant options to acquire capital
stock, which is held by Axys, in certain of Axys' affiliated companies. Axys
internally develops affiliated companies from its ancillary technology and
attempts to ultimately realize value from an affiliated company through the sale
of such affiliated company once it has a well developed business. When adopted
in 1999, the Key Personnel Plan permitted grants of options to acquire capital
stock in Axys Advanced Technologies, Inc., Akkadix Corporation and PPGx, Inc.



     During 2000, the Compensation Committee recommended, and the Board approved
grants of options under the Key Personnel Plan in order to reward key executives
who were instrumental in the development of the affiliated businesses and to
provide incentives to such executives to maximize the value of the affiliated
businesses. By providing incentives to executives to maximize the value of an
affiliated company, Axys is able to provide incentives which, upon the
disposition of the affiliated company, maximizes the value received by Axys.



     The Key Personnel Plan provides that the options granted pursuant to the
plan will vest on a schedule determined by the Board and have an exercise price
which may not be less than Axys' per share investment price in the securities
underlying the options. The Key Personnel Plan also provides that if an
affiliated business is acquired by a third party, the options outstanding with
respect to such affiliated business will automatically vest and the holder of
the option will be granted an option to acquire a pro rata portion of the
consideration received by Axys in the sale transaction. In April 2000, Axys
Advanced Technologies, Inc. was acquired by Discovery Partners International,
Inc. and all outstanding options to acquire shares of capital stock of Axys
Advanced Technologies, Inc. issued under the Key Personnel Plan became fully
vested options to acquire shares of common stock of Discovery Partners
International, Inc. In December 2000, PPGx, Inc. was acquired by DNA Sciences,
Inc. and all outstanding options to acquire shares of capital stock of PPGx,


                                        18
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Inc. issued under the Key Personnel Plan became fully vested options to acquire
shares of capital stock of DNA Sciences, Inc.



     The Compensation Committee recommended and the Board approved grants of
options in 2000 to acquire stock held by Axys in certain of Axys' affiliated
companies, Axys Advanced Technologies, Inc., Akkadix Corporation and PPGx, Inc.,
pursuant to Axys 1999 Key Personnel Stock Option Plan. Each option grant made in
2000 under the Key Personnel Option Plan included a four year vesting period and
an exercise price equal to Axys' per share investment price in the shares
underlying the options. The exercise prices for options granted in 2000 for
shares of capital stock in Axys Advanced Technologies, Inc., Akkadix Corporation
and PPGx, Inc. were $1.00, $3.33 and $6.11 per share, respectively. During 2000,
options to acquire capital stock in such affiliated companies were granted to
the Named Executive Officers and certain other qualifying employees at levels
reflecting, among other things, their respective contributions to such
affiliated companies.


HOW IS THE CHIEF EXECUTIVE OFFICER COMPENSATED?


     John P. Walker. Mr. Walker served as Axys' Chief Executive Officer from
February 1993 until December 31, 2000. Mr. Walker's initial salary, potential
bonus and stock option grants were determined on the basis of negotiations
between the Board and Mr. Walker, while taking into account his experience,
competitive salary information and market conditions at the time. In 1999, the
Company entered into an amended employment agreement with Mr. Walker. Based on
the same criteria described above for all executive officers of the Company, the
Compensation Committee recommended an increase of 3.7% in Mr. Walker's base
salary for 2000 over his 1999 base salary. Other compensation in the form of
forgiveness of indebtedness and the procurement of certain life insurance was
paid in accordance with the terms of Mr. Walker's 1999 employment agreement. In
addition, in accordance with the Company's bonus program outlined above, Mr.
Walker was additionally eligible for a targeted bonus of 50% of his 2000 salary.
The Compensation Committee took into account the extent to which the Company had
achieved its goals in 2000 and, as described above, the Compensation Committee
determined that the Company's performance merited bonus grants of 65% of the
target level for determinations based on Company performance in 2000. As a
result, Mr. Walker was granted a cash bonus of $138,125 which represents 65% of
his targeted bonus of 50% of his 2000 salary. Additionally, in January 2000, the
Compensation Committee recommended and the Board approved the grant of options
to purchase 100,000 shares of the Company's common stock under the 1997 Equity
Incentive Plan, at the fair market value of the Company's common stock on the
grant date in recognition of the Company's and Mr. Walker's other achievements
during 2000. In determining the size of the stock option grant to Mr. Walker,
the Compensation Committee considered the previous grants made to Mr. Walker,
the grants made to other executive officers for 2000 and the desirability of
aligning the interests of Mr. Walker with those of the stockholders. The 100,000
shares subject to the option vest over four years from the grant date at the
rate of 1/48 of the shares subject to the option each month following the grant
date.



     In September 2000, the Board and Mr. Walker agreed that Mr. Walker would
resign as the Chief Executive Officer of Axys upon the appointment of his
successor. After a series of discussions between Mr. Walker, the Compensation
Committee and the Board, it was determined that, in connection with his
agreement to step down as the Chief Executive Officer and in recognition of his
years of service to Axys and the services he would continue to provide Axys as a
non-executive Chairman following his resignation, Mr. Walker's employment
agreement should be amended. Therefore, Mr. Walker and the Company entered into
an amended employment agreement which provides that Mr. Walker will serve as a
non-executive Chairman of Axys for an annual salary of $212,500 beginning
January 1, 2001. The agreement also provides Mr. Walker with other compensation
in the form of forgiveness of indebtedness, the procurement of certain life
insurance and a tax gross-up for tax incurred as a result of the debt
forgiveness. The agreement also provides that Mr. Walker will not, directly or
indirectly, compete with the Company during the term of the agreement and for
two years immediately following the termination of Mr. Walker's employment. For
a more detailed description of the terms of Mr. Walker's employment agreement,
see the section of this proxy statement entitled "Compensation of Executive
Officers -- Management Agreements."


     Paul J. Hastings. In January 2001, Mr. Hastings was appointed as the
Company's President and Chief Executive Officer. Mr. Hastings' initial salary,
potential bonus and stock option grants were determined on the

                                        19
   24


basis of negotiations between the Compensation Committee, the Board and Mr.
Hastings, while taking into account his experience, competitive salary
information and current market conditions. Mr. Hastings' employment agreement
provides for an initial annual base salary of $400,000 and eligibility for an
annual bonus of up to fifty percent of Mr. Hastings' base salary, if Mr.
Hastings achieves certain target goals specified by the Board. In addition, the
Company agreed to loan Mr. Hastings $300,000 pursuant to the terms of a
promissory note with an interest rate of 5.61%, per annum. The note is due and
payable on January 2, 2004, is full-recourse and is secured by shares of the
Company's common stock acquired by Mr. Hastings upon the exercise of any stock
options. If Mr. Hastings continues to provide his services to the Company
through January 2, 2004, the entire principal amount and all accrued interest
under the note will be forgiven by the Company. In connection with his
employment agreement, Mr. Hastings was also granted options to purchase 500,000
shares of common stock at the fair market value on the date of grant which vest
over a four year period. Mr. Hastings was also granted non-statutory performance
options to purchase an additional 100,000 shares of common stock which may vest
over a four year period if certain performance goals are met. In the event such
goals are not met, the entire performance option will vest on the seventh
anniversary of the grant date, subject to Mr. Hastings continued employment at
Axys. In addition, in the event of certain terminations of employment, Mr.
Hastings will continue for one year to receive monthly payments in an amount
equal to one-twelfth of the sum of his base salary plus his target bonus amount
and all stock options held by Mr. Hastings that would have vested within twelve
months of the date of such termination, will immediately and automatically vest.
For a more detailed description of the terms of Mr. Hastings' employment
agreement, see the section of this proxy statement entitled "Compensation of
Executive Officers -- Management Agreements."


HOW HAVE WE RESPONDED TO IRS LIMITS ON DEDUCTIBILITY OF COMPENSATION?


     The Compensation Committee has reviewed the Company's compensation
structure in light of Section 162(m) of the Internal Revenue Code, which limits
the amount of compensation that the Company may deduct in determining its
taxable income for any year to $1,000,000 for any of its five most highly
compensated executive officers. An exception to the limit applies to certain
types of performance-based awards granted under plans approved by the Company's
stockholders, which may include stock options. The Compensation Committee's
policy is to qualify bonus and option grants for the performance-based exception
to the $1,000,000 deduction limitation or to otherwise maintain total
compensation below the deduction limitation whenever possible. In 2000, no
executive officer's compensation exceeded the limitation set by Section 162(m),
except that the aggregate compensation paid to Mr. Walker in 2000 exceeded the
limitation set by Section 162(m); consequently, the Company will not be entitled
to a deduction for any compensation paid to Mr. Walker in 2000 in excess of
$1,000,000.



     Submitted on April 6, 2001 by the members of the Compensation Committee of
the Company's Board of Directors.


                                          Mr. Kailian
                                          Dr. Read

     The above report of the Compensation Committee will not be deemed to be
incorporated by reference to any filing by us under the Securities Act of 1933
or the Securities Exchange Act of 1934, except to the extent that we
specifically incorporate the same by reference.

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             GENERAL DESCRIPTION OF THE 1997 EQUITY INCENTIVE PLAN


     In November 1997, the Axys Board of Directors adopted the 1997 Equity
Incentive Plan (the "Equity Incentive Plan") and reserved 2,500,000 shares of
Axys common stock for issuance thereunder. In 2000, following approval by Axys'
stockholders at last year's annual meeting, an amendment to the Equity Incentive
Plan was adopted which increased the number of shares of common stock available
for issuance thereunder by 1,500,000 shares to 4,000,000 shares. As described in
the second proposal for the annual meeting, the Board is seeking approval to
increase the number of shares of Axys common stock reserved for issuance under
the Equity Incentive Plan by 1,500,000 shares to a total of 5,500,000 shares.


     The Equity Incentive Plan provides for the grant of incentive and
nonstatutory stock options, stock bonuses and restricted stock purchase rights
to eligible employees, officers, directors and consultants. Incentive stock
options granted are intended to qualify as "incentive stock options" within the
meaning of Section 422 of the Internal Revenue Code of 1986, as amended (the
"Code"). Nonstatutory stock options are not intended to qualify as incentive
stock options under the Code.

     Why does Axys offer the Equity Incentive Plan? The purpose of the Equity
Incentive Plan is to attract and retain qualified personnel, to provide
additional incentives to employees, officers, directors and consultants of Axys
and to promote the success of Axys' business. Pursuant to the Equity Incentive
Plan, Axys may grant or issue incentive stock options to employees and officers
and nonstatutory stock options, stock bonuses or stock purchase rights to
employees, officers, consultants and directors.

     Why is Axys Seeking to Increase the Number of Shares Eligible for Issuance
Under the Equity Incentive Plan? Currently, none of the 4,000,000 shares
authorized for issuance under the Equity Incentive Plan are available for future
grants. During 2000 and the first quarter of 2001, Axys had an increased need
for options issued under the Equity Incentive Plan due, in part, to the hiring
of a new Chief Executive Officer. The total current number of shares available
for issuance under the Equity Incentive Plan represents 10.7% of Axys'
outstanding common stock as of February 28, 2001. If the amendment is approved
by the stockholders, the 5,500,000 shares available for issuance under the
Equity Incentive Plan will represent 14.7% of Axys' outstanding common stock as
of February 28, 2001. The additional authorized shares are necessary in order
for Axys to attract and retain qualified personnel and to continue to provide
additional incentives to its current employees, officers, directors and
consultants.

     Who is in charge of the Equity Incentive Plan? The Equity Incentive Plan is
administered by the Board of Directors. The Axys Board of Directors has the
power to construe and interpret the Equity Incentive Plan and, subject to the
provisions of the Equity Incentive Plan, to determine the persons to whom and
the dates on which awards will be granted, the number of shares to be subject to
each award, the time or times during the term of each award within which all or
a portion of such award may be exercised, the exercise price, the type of
consideration and other terms of the award. The Axys Board of Directors is
authorized to delegate administration of the Equity Incentive Plan to one or
more committees and has delegated such authority to the Compensation Committee
and, for grants to employees other than executive officers, the Option
Committee. As used herein with respect to the Equity Incentive Plan, the "Axys
Board of Directors" refers to the Compensation Committee and the Option
Committee, as well as to the Axys Board of Directors itself.

     Axys currently limits the directors who may serve as members of the
Compensation Committee to those who are "outside directors," as such term is
defined in Section 162(m) of the Code. This limitation excludes from the
Compensation Committee (i) current employees of Axys, (ii) former employees of
Axys receiving compensation for past services (other than benefits under a
tax-qualified retirement plan), (iii) current and former officers of Axys and
(iv) directors currently receiving direct or indirect compensation from Axys in
any capacity (other than as a director); unless any such person described above
is otherwise considered an "outside director" under applicable federal
regulations under the Code.

     Who is Eligible to Participate in the Equity Incentive Plan? Generally
speaking, employees, officers, directors and certain consultants of Axys and its
parents and subsidiaries (as defined in Section 424(e) of the Code)
("Affiliates") are eligible to participate in the Equity Incentive Plan.

                                        21
   26

     Notwithstanding the foregoing, no incentive stock option may be granted
under the Equity Incentive Plan to any person who, at the time of the grant,
owns (or is deemed to own) stock possessing more than 10% of the total combined
voting power of Axys or any Affiliate of Axys, unless the option exercise price
is at least 110% of the fair market value of the stock subject to the option at
the date of grant, and the term of the option does not exceed five years from
the date of grant. In addition, the aggregate fair market value, determined at
the time of grant, of the shares of common stock with respect to which incentive
stock options are exercisable for the first time by an optionee during any
calendar year (under all such plans of Axys and its Affiliates) may not exceed
$100,000.


     Under the Equity Incentive Plan, no individual may be granted options
covering more than 500,000 shares of common stock in any calendar year. The
purpose of such a per-employee limitation is to comply with regulations under
the Code that permit certain performance-based compensation, including
compensation attributable to stock options that meet specified criteria, to be
exempt from the $1,000,000 limitation under Section 162(m) of the Code on the
amount that may be deducted by publicly held corporations for compensation paid
to certain employees. See "What are the Tax Implications to Participants in the
Equity Incentive Plan?" below. Axys does not currently have any intention of
granting such number of options to any individual. There can be no assurance,
however, that the Axys Board of Directors will not determine in some future
circumstances that it would be in the best interests of Axys and its
stockholders to grant options to purchase such number of shares to a single
employee during a calendar year.


     What are the terms of the Options granted?

     Exercise Price; Payment. The exercise price of stock options granted under
the Equity Incentive Plan may not be less than the fair market value of the
common stock subject to the option on the date of the option grant, and in the
case of incentive stock options granted to certain individuals (see "Who is
Eligible to Participate in the Equity Incentive Plan" above), may not be less
than 110% of such fair market value.

     The exercise price of options granted under the Equity Incentive Plan must
be paid either: (a) in cash at the time the option is exercised; or (b) at the
discretion of the Axys Board of Directors: (i) by delivery of other common stock
of Axys, (ii) pursuant to a deferred payment arrangement, or (iii) in any other
form of legal consideration acceptable to the Axys Board of Directors.

     Option Exercise. Options granted under the Equity Incentive Plan may become
exercisable in cumulative increments ("vest") as determined by the Axys Board of
Directors. Shares covered by currently outstanding options under the Equity
Incentive Plan typically vest at the rate of 12.5% of the shares subject to the
option at the end of the first six months and 1/42 of the shares subject to the
option each month for 42 months thereafter, for initial grants to employees.
Subsequent grants to employees generally vest monthly over 48 months. Shares
covered by options granted in the future under the Equity Incentive Plan may be
subject to different vesting terms. The Axys Board of Directors has the power to
accelerate the time during which an option may be exercised. To the extent
provided by the terms of an option, an optionee may satisfy any federal, state
or local tax withholding obligation relating to the exercise of such option by a
cash payment upon exercise, by authorizing Axys to withhold a portion of the
stock otherwise issuable to the optionee, by delivering already owned stock of
Axys or by a combination of these means.

     Term. The maximum term of options granted under the Equity Incentive Plan
is 10 years, except that, in the case of incentive stock options granted to
certain individuals (see "Who is Eligible to Participate in the Equity Incentive
Plan"), the maximum term is five years. Options under the Equity Incentive Plan
terminate ninety (90) days after termination of the optionee's employment or
relationship as a consultant or director of Axys or any Affiliate of Axys,
unless (a) such termination is due to such person's permanent and total
disability (as defined in the Code), in which case the option may, but need not,
provide that it may be exercised at any time within twelve (12) months of such
termination; (b) the optionee dies while employed by or serving as a consultant
of Axys or any Affiliate of Axys, or within ninety (90) days after termination
of such relationship, in which case the option may, but need not, provide that
it may be exercised (to the extent the option was exercisable at the time of the
optionee's death) within twelve (12) months of the optionee's death by the
person or persons to whom the rights to such option pass by will or by the laws
of descent and distribution; or (c) the option by its terms specifically
provides otherwise. In any event an Option is not

                                        22
   27

exercisable for a period longer than the term of such Option as set forth in the
agreement evidencing the Option. Individual options by their terms may provide
for exercise within a longer period of time following termination of employment
or the consultant or director relationship. The option term may also be extended
in the event that exercise of the option within these periods is prohibited for
specified reasons.

     What Are the Other Forms of Awards Granted Under the Plan?

     Restricted Stock Awards. A restricted stock award is an award typically for
a fixed number of shares of common stock subject to restrictions. The Axys Board
of Directors specifies the price, if any, the participant must pay for such
shares and the restrictions (which may include, for example, continued service
only and/or performance standards) imposed on such shares.

     Stock Bonuses. The Axys Board of Directors may grant a stock bonus to any
eligible person to reward exceptional or special services, contributions or
achievements in the manner and on such terms and conditions (including any
restrictions on such shares) as determined from time to time by the Axys Board
of Directors. The number of shares so awarded shall be determined by the Axys
Board of Directors.

     What Happens if There is a Change in the Stock Subject to the Equity
Incentive Plan? If there is any change in the stock subject to the Equity
Incentive Plan or subject to any option granted under the Equity Incentive Plan
(through merger, consolidation, reorganization, recapitalization, stock
dividend, dividend in property other than cash, stock split, liquidating
dividend, combination of shares, exchange of shares, change in corporate
structure or otherwise), the Equity Incentive Plan and options outstanding
thereunder will be appropriately adjusted as to the class and the maximum number
of shares subject to such plan, the maximum number of shares which may be
granted to an employee during a calendar year, and the class, number of shares
and price per share of stock subject to such outstanding options.

     What Happens in the Event of Certain Corporate Transactions? The Equity
Incentive Plan provides that, in the case of certain corporate events,
outstanding options under the Equity Incentive Plan will be assumed or
equivalent options substituted by each successor corporation or a parent or
subsidiary of such successor corporation or in the event that the successor
corporation refuses to assume or replace, then such options shall accelerate and
become immediately exercisable in full and will subsequently terminate if not
exercised prior to the completion of the corporate transaction. Generally, such
corporate events include a 50% or more change in ownership of the Company,
certain mergers or consolidations, or liquidation or dissolution of the Company
or sale of substantially all of the Company's assets.

     What is the Duration of the Equity Incentive Plan and Can it Be Amended or
Terminated? The Axys Board of Directors may suspend or terminate the Equity
Incentive Plan without stockholder approval at any time. Unless sooner
terminated, the Equity Incentive Plan will terminate in November 2007.

     The Axys Board of Directors may also amend the Equity Incentive Plan at any
time or from time to time. However, no amendment will be effective unless
approved by the stockholders of Axys within twelve months before or after its
adoption by the Axys Board of Directors if such modification requires
stockholder approval in order to comply with Rule 16b-3 promulgated under the
Exchange Act, or satisfy the requirements of Section 422 of the Code or any
Nasdaq or securities exchange listing requirements. The Axys Board of Directors
may submit any other amendment to the Equity Incentive Plan for stockholder
approval, including, but not limited to, amendments intended to satisfy the
requirements of Section 162(m) of the Code regarding the exclusion of
performance-based compensation from the limitation on the deductibility of
compensation paid to certain employees. Additionally, the Board may amend the
Plan in any manner it deems necessary or advisable in order to provide eligible
employees, directors or consultants with the maximum benefits provided or to be
provided under the Code and any regulations promulgated thereunder with respect
to incentive stock options or to bring the Equity Incentive Plan or incentive
stock options into compliance with the Code.

     What are the Tax Implications to Participants in the Equity Incentive Plan?

     Incentive Stock Options. Incentive stock options under the Equity Incentive
Plan are intended to be eligible for the favorable federal income tax treatment
accorded "incentive stock options" under the Code.

                                        23
   28

     There generally are no federal income tax consequences to the optionee or
Axys by reason of the grant or exercise of an incentive stock option. However,
the exercise of an incentive stock option may result in the imposition of or an
increase in liability of the optionee under the alternative minimum tax rules.

     If an optionee holds stock acquired through exercise of an incentive stock
option for more than two years from the date on which the option is granted and
more than one year from the date on which the shares are transferred to the
optionee upon exercise of the option, any gain or loss on a disposition of such
stock will be a capital gain or loss. Generally, if the optionee disposes of the
stock before the expiration of either of these holding periods (a "disqualifying
disposition"), at the time of disposition the optionee will recognize taxable
ordinary income equal to the lesser of (i) the excess of the stock's fair market
value on the date of exercise over the exercise price, or (ii) the optionee's
actual gain, if any, on the purchase and sale. The optionee's additional gain,
or any loss, upon the disqualifying disposition will be a capital gain or loss.
Capital gains currently are generally subject to lower tax rates than ordinary
income. The maximum capital gains rate for federal income tax purposes is
currently 28% while the maximum ordinary income rate is effectively 39.6% at the
present time. Slightly different rules may apply to optionees who acquire stock
subject to certain repurchase options or who are subject to Section 16(b) of the
Exchange Act.

     To the extent the optionee recognizes ordinary income by reason of a
disqualifying disposition, Axys will generally be entitled (subject to the
requirement of reasonableness, the provisions of Section 162(m) of the Code and
the satisfaction of a tax reporting obligation) to a corresponding business
expense deduction in the tax year in which the disqualifying disposition occurs.

     Nonstatutory Stock Options. Nonstatutory stock options granted under the
Equity Incentive Plan generally have the following federal income tax
consequences:

     There are no tax consequences to the optionee or Axys by reason of the
grant of a nonstatutory stock option. Upon exercise of a nonstatutory stock
option, the optionee normally will recognize taxable ordinary income equal to
the excess of the stock's fair market value on the date of exercise over the
option exercise price. Generally, with respect to employees, Axys is required to
withhold from regular wages or supplemental wage payments an amount based on the
ordinary income recognized. Subject to the requirement of reasonableness, the
provisions of Section 162(m) of the Code and the satisfaction of a tax reporting
obligation, Axys will generally be entitled to a business expense deduction
equal to the taxable ordinary income realized by the optionee. Upon disposition
of the stock, the optionee will recognize a capital gain or loss equal to the
difference between the selling price and the sum of the amount paid for such
stock plus any amount recognized as ordinary income upon exercise of the option.
Slightly different rules may apply to optionees who acquire stock subject to
certain repurchase options or who are subject to Section 16(b) of the Exchange
Act.

     Stock Bonuses and Restricted Stock. Stock bonuses and restricted stock
granted under the Equity Incentive Plan generally has the following federal
income tax consequences:

     Upon acquisition of stock under a stock bonus award the recipient normally
will recognize taxable ordinary income equal to the excess of the stock's fair
market value over the purchase price, if any. With respect to nontransferable
restricted stock subject to a substantial risk of forfeiture, the recipient will
recognize ordinary income on the stock equal to the excess of the fair market
value of the stock over the price paid, if any, only at the time the
restrictions lapse (unless the recipient elects to accelerate recognitions as of
the date of grant). With respect to employees, Axys is required to withhold from
regular wages or supplemental wage payments an amount based on the ordinary
income recognized. Subject to the requirement of reasonableness, the provisions
of Section 162(m) of the Code and the satisfaction of a tax reporting
obligation, Axys will generally be entitled to a business expense deduction
equal to the taxable ordinary income realized by the recipient. Upon disposition
of the stock, the recipient will recognize a capital gain or loss equal to the
difference between the selling price and the sum of the amount paid for such
stock, if any, plus any amount recognized as ordinary income upon acquisition
(or vesting) of the stock. Slightly different rules may apply to persons who
acquire stock subject to forfeiture under Section 16(b) of the Exchange Act.

     Potential Limitation on Company Deductions. Section 162(m) of the Code
denies a deduction to any publicly held corporation for compensation paid to
certain employees in a taxable year to the extent that

                                        24
   29

compensation exceeds $1,000,000 for a covered employee. It is possible that
compensation attributable to awards under the Equity Incentive Plan, when
combined with all other types of compensation received by a covered employee
from Axys, may cause this limitation to be exceeded in any particular year.

     Certain kinds of compensation, including qualified "performance-based
compensation," are disregarded for purposes of the deduction limitation. In
accordance with Department of Treasury regulations issued under Section 162(m)
of the Code, compensation attributable to stock options will qualify as
performance-based compensation, provided that: (i) the stock award plan contains
a per-employee limitation on the number of shares for which stock options may be
granted during a specified period; (ii) the per-employee limitation is approved
by the stockholders; (iii) the award is granted by a compensation committee
comprised solely of outside directors; and (iv) the exercise price of the award
is no less than the fair market value of the stock on the date of grant.
Restricted stock qualifies as performance-based compensation under these
Department of Treasury regulations only if: (i) the award is granted by a
compensation committee comprised solely of "outside directors"; (ii) the award
is granted (or exercisable) only upon the achievement of an objective
performance goal established in writing by the compensation committee while the
outcome is substantially uncertain: (iii) the compensation committee certifies
in writing prior to the granting (or exercisability) of the award that the
performance goal has been satisfied; and (iv) prior to the granting (or
exercisability) of the award, stockholders have approved the material terms of
the award (including the class of employees eligible for such award, the
business criteria on which the performance goal is based, and the maximum amount
(or formula used to calculate the amount) payable upon attainment of the
performance goal).

                AMENDMENT TO AXYS' CERTIFICATE OF INCORPORATION


     The Board is requesting approval of an amendment to the Company's Restated
Certificate of Incorporation to increase the number of the Company's authorized
shares of common stock by 50 million shares to a total of 100 million shares. A
copy of this amendment is attached to this proxy statement as Appendix B.



     The additional common stock to be authorized by adoption of the amendment
would be part of the existing class of the Company's common stock and, if and
when issued, would have rights and privileges identical to the currently
outstanding shares of common stock of the Company. Adoption of the proposed
amendment and issuance of the common stock would not affect the rights of the
holders of currently outstanding common stock, except for effects incidental to
increasing the number of shares of the common stock outstanding, such as
dilution of the earnings per share and voting rights of current holders of
common stock. The amendment would become effective upon the filing of a
Certificate of Amendment of the Company's Restated Certificate of Incorporation
with the Secretary of State of the State of Delaware. If the amendment is
adopted, the Company intends to file the Certificate of Amendment as soon as
practicable after stockholder approval is obtained and expects that the filing
would be made on or about May 15, 2001.



     Axys is seeking to increase the number of authorized shares of its common
stock from 50 million to 100 million shares in order to provide the Company with
the ability to enter into future transactions which would require the issuance
of common stock, as well as permit the exercise or conversion of all outstanding
and future convertible securities. As of February 28, 2001, approximately 37.4
million of the 50 million authorized shares of common stock were outstanding. As
of February 28, 2001, on a fully-diluted basis (which assumes the exercise of
all outstanding options and warrants and the conversion of all convertible
securities), approximately 48.5 million of the 50 million shares of authorized
common stock were outstanding. Axys believes an increase in the number of shares
of authorized common stock is necessary in order to have enough authorized
shares to reserve for the future exercise of all outstanding options and
warrants, the conversion of all convertible securities, and for capital
financing transactions or other transactions which may require the issuance of
shares of common stock.


     The Board has no present plans for issuing any of the additional shares of
common stock which would be authorized by the amendment except as would be
required in connection with common stock presently reserved for issuance
pursuant to outstanding options, warrants and other convertible securities.

                                        25
   30


     Although at present the Board has no plans to issue additional shares of
common stock in excess of the number previously authorized, it believes it is
desirable to have such shares available to provide additional flexibility to use
its capital stock for business and financial purposes in the future. The
additional shares may be used, without further stockholder approval, except as
may be required by law, regulatory authorities and the Nasdaq Stock Market or
any other stock exchange on which the Company's shares may then be listed. The
additional shares may be used for various purposes including, without
limitation, stock splits and dividends, raising capital, paying interest in
common stock on the Company's convertible debt, providing equity incentives to
employees, officers or directors, establishing strategic relationships with
other companies and expanding the Company's business or research and development
programs through the acquisition of other businesses or technologies.



     The existence of additional authorized shares of common stock could have
the effect of rendering more difficult or discouraging hostile takeover
attempts. The Company is not aware of any existing or planned effort on the part
of any party to accumulate material amounts of voting stock, or to acquire the
Company by means of a merger, tender offer, solicitation of proxies in
opposition to management or otherwise, or to change the Company's management,
nor is the Company aware of any person having made any offer to acquire the
voting stock or assets of the Company.


     If the amendment to the Certificate of Incorporation is approved by the
stockholders at the annual meeting, the first paragraph of Article Fourth of the
Company's Certificate of Incorporation, as amended, would read in full as
follows:

          "FOURTH: The total number of shares of capital stock that the
     Corporation shall have the authority to issue shall be 110,000,000 shares,
     all of which shall be divided into two (2) classes: Preferred Stock, to
     consist of 10,000,000 shares, par value $.001 per share and Common Stock,
     to consist of 100,000,000 shares, par value $.001 per share."

                                        26
   31

                             AUDIT COMMITTEE REPORT

     The Audit Committee of the Axys Pharmaceuticals, Inc. Board of Directors is
comprised of independent directors as required by the listing standards of the
Nasdaq National Market. The current members of the Audit Committee are Mr.
Lerner (Chairman), Dr. Arvin and Mr. Mendelson. The members in 2000 were Mr.
Lerner (Chairman), Dr. Arvin, and Dr. Kennedy. Dr. Kennedy resigned from the
Board of Directors and the Audit Committee in December 2000. Mr. Mendelson
replaced Dr. Kennedy in February 2001. The Audit Committee operates pursuant to
a written charter adopted by the Board of Directors, a copy of which is attached
to this proxy statement as Appendix A.

     The role of the Audit Committee is to oversee the Company's financial
reporting process on behalf of the Board of Directors. Management of the Company
has the primary responsibility for the Company's financial statements as well as
the Company's financial reporting process, principles and internal controls. The
independent auditors are responsible for performing an audit of the Company's
financial statements and expressing an opinion as to the conformity of such
financial statements with generally accepted accounting principles.

     In this context, the Audit Committee has reviewed and discussed the audited
financial statements of the Company as of and for the year ended December 31,
2000 with management and the independent auditors. The Audit Committee has
discussed with the independent auditors the matters required to be discussed by
the Statement on Auditing Standards No. 61 (Communication with Audit
Committees), as currently in effect. In addition, the Audit Committee has
received the written disclosures and the letter from the independent auditors
required by Independence Standards Board Standard No. 1 (Independence
Discussions with Audit Committees), as currently in effect, and it has discussed
with the auditors their independence from the Company. The Audit Committee has
also considered whether the independent auditors' provision of non-audit
services to the Company is compatible with maintaining the auditors'
independence.

     The members of the Audit Committee are not engaged in the accounting or
auditing profession and, consequently, are not experts in matters involving
auditing or accounting. In the performance of their oversight function, the
members of the Audit Committee necessarily relied upon the information,
opinions, reports and statements presented to them by management of the Company
and by the independent auditors. As a result, the Audit Committee's oversight
and the review and discussions referred to above do not assure that management
has maintained adequate financial reporting processes, principles and internal
controls, that the Company's financial statements are accurate, that the audit
of such financial statements has been conducted in accordance with generally
accepted auditing standards or that the Company's auditors meet the applicable
standards for auditor independence.

     Based on the reports and discussions described above, the Audit Committee
recommended to the Board of Directors that the audited financial statements be
included in the Company's Annual Report on Form 10-K for the year ended December
31, 2000, for filing with the SEC.


     Submitted on April 6, 2001 by the members of the Audit Committee of the
Company's Board of Directors.


                                          Mr. Lerner (Chairman)
                                          Dr. Arvin
                                          Mr. Mendelson

     The above report of the Audit Committee will not be deemed to be
incorporated by reference to any filing by us under the Securities Act of 1933
or the Securities Exchange Act of 1934, except to the extent that we
specifically incorporate the same by reference.

                                        27
   32

                     APPOINTMENT OF INDEPENDENT ACCOUNTANTS


     Subject to ratification by the stockholders, the Board of Directors has
reappointed the firm of Ernst & Young LLP, independent auditors, to audit the
financial statements of the Company for the fiscal year ending December 31,
2001. A representative of Ernst & Young LLP is expected to be present at the
annual meeting to respond to appropriate questions, and will be given the
opportunity to make a statement if he or she so desires.



     In the event the stockholders fail to ratify the appointment, the Board
will reconsider its selection. Even if the selection is ratified, the Board in
its discretion may direct the appointment of a different independent accounting
firm at any time during the year if the Board feels that such a change would be
in the best interest of the Company and its stockholders.



     Ernst & Young LLP has served as independent auditors to the Company for the
fiscal year ended December 31, 2000. Fees for the audit for the fiscal year
ended December 31, 2000 were $185,000 and all other fees were $400,000,
including audit related services of $258,000 and non-audit services of $142,000.
Audit related services include fees for accounting consultation and SEC
registration statements. There were no fees paid to Ernst & Young LLP for
financial information system design and implementation services. The Audit
Committee has considered whether the provision of these non-audit services is
compatible with maintaining the principal accountants' independence.


            SECTION 16(a) BENEFICIAL OWNERSHIP REPORTING COMPLIANCE

     Section 16(a) of the Exchange Act requires directors, executive officers
and holders of more than 10% of Axys' common stock to file reports with the SEC
regarding their ownership and changes in ownership of Axys' common stock. Such
persons are required by regulations promulgated by the SEC to furnish the
Company with copies of all Section 16(a) forms they file.

     To the Company's knowledge, based solely on its review of copies of such
reports received by the Company or written representations from certain
reporting persons that no other reports were required, during the year ended
December 31, 2000, all of the Company's directors and executive officers and
persons who own more than 10% of the common stock have complied with the
reporting requirements of Section 16(a), except that Douglas H. Altschuler
failed to timely file a Form 3 after he joined Axys in December 2000 as its Vice
President and General Counsel.

              RELATIONSHIPS AND TRANSACTIONS YOU SHOULD KNOW ABOUT


     In 1997, the Company advanced $750,000 in a note receivable to John P.
Walker, the Company's Chief Executive Officer during 2000 until December 31,
2000 and a nominee for director. The note, when it was outstanding, bore
interest at the rate of 6.02% per year until 1999 when the interest rate was
reduced to 4.71% per year. The note was full recourse and secured by shares of
Axys common stock owned by Mr. Walker. In December 2000, the Company amended the
1999 employment agreement with Mr. Walker. Under the terms of the agreement, Mr.
Walker will receive approximately one-half of his former salary and bonus,
forgiveness of his note receivable plus accrued interest at December 31, 2000,
in exchange for three years of continued service and an agreement not to
compete. The agreement is in effect through December 31, 2003. The Company
charged compensation expense in 2000 for the forgiveness of the note receivable.
For a more detailed discussion of Mr. Walker's employment agreement see the
section of this proxy statement entitled "Compensation of Executive
Officers -- Management Agreements."



     In August 2000, the Company advanced $300,000 in a note receivable to Dr.
Michael C. Venuti for housing assistance. The note earns interest at 6.37% per
year and interest is due annually. The note plus accrued interest is forgivable
over five years, subject to Dr. Venuti's continued employment with Axys.



     In January 2000, the Company advanced $300,000 in a note receivable to Paul
J. Hastings. The note earns interest at 5.61% per annum. The note is due and
payable on January 2, 2004, is full-recourse and is secured by shares of common
stock that Mr. Hastings acquires upon the exercise of any stock options. The
entire note will be forgiven by the Company if Mr. Hastings continues to provide
his services to the Company through January 2, 2004.


                                        28
   33

                               PERFORMANCE GRAPH


     The graph below shows a five-year comparison of cumulative total returns
from an initial $100 investment in Axys, the Nasdaq Composite and the AMEX
Biotechnology Index. All values include reinvestment of dividends, except for
Axys' values because Axys has never paid dividends. On April 9, 2001, the
closing price per share of Axys' common stock was $2.96, as reported by the
Nasdaq National Market.

[PERFORMANCE GRAPH]



                                                AXYS PHARMACEUTICALS INC.        NASDAQ US INDEX        AMEX BIOTECHNOLOGY INDEX
                                                -------------------------        ---------------        ------------------------
                                                                                               
Dec 95                                                   100.00                      100.00                      100.00
Dec 96                                                   100.00                      122.71                      107.87
Dec 97                                                    62.04                      149.25                      121.42
Dec 98                                                    43.52                      209.28                      138.40
Dec 99                                                    30.09                      386.77                      292.62
Dec 00                                                    41.66                      234.81                      496.61



                                 OTHER MATTERS


     As of the date of this proxy statement, the Board of Directors knows of no
other matters that will be presented for consideration at the annual meeting. If
any other matters are properly brought before the meeting, it is the Board's
intention to vote on such matters in accordance with their best judgment.

                                          By Order of the Board of Directors,

                                          /s/ DOUGLAS H. ALTSCHULER

                                          Douglas H. Altschuler
                                          Vice President and General Counsel


April 16, 2001


                                        29
   34

                                   APPENDIX A
                           AXYS PHARMACEUTICALS, INC.

                            AUDIT COMMITTEE CHARTER

ORGANIZATION

     This charter governs the operations of the audit committee. The committee
shall review and reassess the charter at least annually and obtain the approval
of the board of directors. The committee shall be appointed by the board of
directors and shall comprise at least three directors, each of whom are
independent of management and the Company. Members of the committee shall be
considered independent if they have no relationship that may interfere with the
exercise of their independence from management and the Company. All committee
members shall be financially literate, or shall become financially literate
within a reasonable period of time after appointment to the committee, and at
least one member shall have accounting or related financial management
expertise.

STATEMENT OF POLICY

     The audit committee shall provide assistance to the board of directors in
fulfilling their oversight responsibility to the stockholders, potential
stockholders, the investment community, and others relating to the Company's
financial statements and the financial reporting process, the systems of
internal accounting and financial controls, the internal audit function, the
annual independent audit of the Company's financial statements, and such legal
compliance and ethics programs as may be established by management and the
board. In so doing, it is the responsibility of the committee to maintain free
and open communication between the committee, independent auditors, and
management of the Company. In discharging its oversight role, the committee is
empowered to investigate any matter brought to its attention with full access to
all books, records, facilities, and personnel of the Company and the power to
retain outside counsel or other experts for this purpose.

RESPONSIBILITIES AND PROCESSES

     The primary responsibility of the audit committee is to oversee the
Company's financial reporting process on behalf of the board and report the
results of their activities to the board. Management is responsible for
preparing the Company's financial statements, and the independent auditors are
responsible for auditing those financial statements. The committee in carrying
out its responsibilities believes its policies and procedures should remain
flexible, in order to best react to changing conditions and circumstances. The
committee should take the appropriate actions to set the overall corporate
"tone" for quality financial reporting, sound business risk practices, and
ethical behavior.

     The following shall be the principal recurring processes of the audit
committee in carrying out its oversight responsibilities. The processes are set
forth as a guide with the understanding that the committee may supplement them
as appropriate.

     - The committee shall have a clear understanding with management and the
       independent auditors that the independent auditors are ultimately
       accountable to the board and the audit committee, as representatives of
       the Company's shareholders. The committee shall have the ultimate
       authority and responsibility to evaluate and, where appropriate, replace
       the independent auditors. The committee shall discuss with the auditors
       their independence from management and the Company and the matters
       included in the written disclosures required by the Independence
       Standards Board. Annually, the committee shall review and recommend to
       the board the selection of the Company's independent auditors, subject to
       stockholder approval.

     - The committee shall discuss with the independent auditors the overall
       scope and plans for their respective audits including the adequacy of
       staffing and compensation. Also, the committee shall discuss with
       management, and the independent auditors the adequacy and effectiveness
       of the

                                       A-1
   35

       accounting and financial controls, including the Company's system to
       monitor and manage business risk, and any legal and ethical compliance
       programs.

       Further, the committee shall meet separately with the independent
       auditors, with and without management present, to discuss the results of
       their examinations.

     - The committee shall review the interim financial statements with
       management and the independent auditors prior to the filing of the
       Company's Quarterly Report on Form 10-Q. Also, the committee shall
       discuss the results of the quarterly review and any other matters
       required to be communicated to the committee by the independent auditors
       under generally accepted auditing standards. The chair of the committee
       may represent the entire committee for the purpose of this review.

     - The committee shall review with management and the independent auditors
       the financial statements to be included in the Company's Annual Report on
       Form 10-K (or the annual report to shareholders if distributed prior to
       the filing of Form 10-K), including their judgment about the quality, not
       just acceptability, of accounting principles, the reasonableness of
       significant judgments, and the clarity of the disclosures in the
       financial statements. Also, the committee shall discuss the results of
       the annual audit and any other matters required to be communicated to the
       committee by the independent auditors under generally accepted auditing
       standards.

                                       A-2
   36

                                                                      APPENDIX B

                            CERTIFICATE OF AMENDMENT
                                       OF
                     RESTATED CERTIFICATE OF INCORPORATION
                                       OF
                          AXYS PHARMACEUTICALS, INC.,
                             A DELAWARE CORPORATION

     Axys Pharmaceuticals, Inc., a corporation organized and existing under and
by virtue of the General Corporation Law of the State of Delaware (this
"Corporation"), DOES HEREBY CERTIFY:

          1. That the Board of Directors of this Corporation adopted a
     resolution setting forth a proposed amendment of the Restated Certificate
     of Incorporation of this Corporation. The resolution setting forth the
     proposed amendment is as follows:

             "NOW, THEREFORE, BE IT RESOLVED, that the Restated Certificate of
        Incorporation of this Corporation by amending the first paragraph of
        Article FOURTH, so that, as amended, the first paragraph of Article
        FOURTH shall read in its entirety as follows:

             FOURTH: The total number of shares of capital stock that the
        Corporation shall have the authority to issue shall be 110,000,000
        shares, all of which shall be divided into two (2) classes: Preferred
        Stock, to consist of 10,000,000 shares, par value $.001 per share and
        Common Stock, to consist of 100,000,000 shares, par value $.001 per
        share."

          2. This Certificate of Amendment of Restated Certificate of
     Incorporation was duly adopted and approved by the stockholders of this
     Corporation in accordance with the provisions of Section 242 of the
     Delaware General Corporation Law.

     IN WITNESS WHEREOF the undersigned has caused this Certificate of Amendment
of Restated Certificate of Incorporation to be duly executed as of the
               day of May, 2001, and hereby affirm and acknowledge under penalty
of perjury that the filing of this Certificate of Amendment of Restated
Certificate of Incorporation of Axys Pharmaceuticals, Inc. is the act and deed
of Axys Pharmaceuticals, Inc.

                                          AXYS PHARMACEUTICALS, INC.,
                                          a Delaware corporation

                                          By:
                                            ------------------------------------

                                       B-1
   37

                                                                      APPENDIX C

                               DIRECTIONS TO AXYS

FROM THE NORTH (SAN FRANCISCO):

- - Take 101 South to the Grand Avenue exit.

- - At the first stop light, turn left on Airport Boulevard.

- - Turn left at the next stop light onto East Grand Avenue.

- - Continue east until you reach Kimball Way (approximately 1 mile).

- - Make a right turn on Kimball Way and you will be at 180 Kimball Way, a
  two-story gray and blue building.

FROM THE SOUTH (SAN FRANCISCO INTERNATIONAL AIRPORT):

- - Take 101 North to South San Francisco Grand Avenue exit (about 3 miles).

- - Turn right at the end of the off ramp.

- - Continue to follow East Grand Avenue for approximately 1 mile, passing two
  stoplights.

- - Make a right turn on Kimball Way and you will be at 180 Kimball Way, a
  two-story gray and blue building.

                                       C-1
   38

                           AXYS PHARMACEUTICALS, INC.
           PROXY SOLICITED ON BEHALF OF THE BOARD OF DIRECTORS FOR THE
            ANNUAL MEETING OF STOCKHOLDERS TO BE HELD ON MAY 14, 2001

        The undersigned hereby appoints Paul J. Hastings and Douglas H.
Altschuler, and each of them, as proxies, each with the power to appoint his
substitute, and hereby authorizes either of them to act and to vote at the
annual meeting of stockholders of AXYS PHARMACEUTICALS, INC. (the "Company") to
be held on May 14, 2001, and at any adjournments thereof, as indicated upon all
matters referred to on this proxy card and described in the proxy statement for
the meeting, and, in their discretion, upon any other matters which may properly
come before the meeting.

        1.     ELECT JOHN P. WALKER, ANN M. ARVIN, M.D., VAUGHN M. KAILIAN, PAUL
               J. HASTINGS, IRWIN LERNER, ALAN C. MENDELSON, J.D., AND J.
               LEIGHTON READ, M.D. TO THE BOARD OF DIRECTORS OF THE COMPANY.

                   [ ] FOR ALL nominees           [ ] WITHHOLD AUTHORITY
                   listed above (except as           to vote for all
                   marked to the contrary).          nominees listed above.

                         (Instruction: To WITHHOLD AUTHORITY to vote
                         for any nominee, draw a line through the
                         nominee's name in the list above.

        2.     PROPOSAL TO APPROVE THE AMENDMENT OF THE COMPANY'S 1997 EQUITY
               INCENTIVE PLAN TO INCREASE THE NUMBER OF SHARES OF COMMON STOCK
               RESERVED FOR ISSUANCE THEREUNDER BY 1,500,000 SHARES.

                          [ ] FOR     [ ] AGAINST     [ ] ABSTAIN

        3.     PROPOSAL TO APPROVE THE AMENDMENT OF THE COMPANY'S CERTIFICATE OF
               INCORPORATION TO INCREASE THE NUMBER OF AUTHORIZED SHARES OF THE
               COMPANY'S COMMON STOCK BY 50,000,000 SHARES.

                          [ ] FOR     [ ] AGAINST     [ ] ABSTAIN

        4.     RATIFICATION OF THE APPOINTMENT OF ERNST & YOUNG LLP AS THE
               COMPANY'S INDEPENDENT AUDITORS FOR THE FISCAL YEAR ENDING
               DECEMBER 31, 2001.

                          [ ] FOR     [ ] AGAINST     [ ] ABSTAIN

        Shares represented by all properly executed proxies will be voted in
accordance with instructions appearing on this proxy card and in the discretion
of the proxy holders as to any other matter that may properly come before the
meeting. IN THE ABSENCE OF SPECIFIC INSTRUCTIONS, PROXIES WILL BE VOTED FOR
PROPOSALS 1, 2, 3 AND 4.

Dated: _______________, 2001

                                    (Signature)


                                    (Signature)

                                    Please sign as name(s) appears on this proxy
                                    card, and date this proxy card. If a joint
                                    account, each joint owner must sign. If
                                    signing for a corporation or partnership as
                                    agent, attorney or fiduciary, indicate the
                                    capacity in which you are signing.