AUTOIMMUNE INC
DEF 14A, 2000-04-13
BIOLOGICAL PRODUCTS, (NO DIAGNOSTIC SUBSTANCES)
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<PAGE>

                           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 [_]

Check the appropriate box:

[_] Preliminary Proxy Statement           [_] Confidential, for Use of the
                                              Commission Only (as permitted by
                                              Rule 14a-6(e)(2))

[X] Definitive Proxy Statement

[_] Definitive Additional Materials

[_] Soliciting Material Pursuant to (S)240.14a-11(c) or (S)240.14a-12

                                AutoImmune Inc.
             -----------------------------------------------------
               (Name of Registrant as Specified In Its Charter)

                                AutoImmune Inc.
             -----------------------------------------------------
                  (Name of Person(s) Filing Proxy Statement)

Payment of Filing Fee (Check the appropriate box):

[X] No fee required.

[_] $125 per Exchange Act Rules 0-11(c)(1)(ii), 14a-6(i)(1), 14a-6(i)(2) or
    Item 22(a)(2) of Schedule 14A.

[_] Fee computed on table below per Exchange Act Rules 14a-6(i)(4) and 0-11.

    1) Title of each class of securities to which transaction applies:

    2) Aggregate number of securities to which transaction applies:

    3) Per unit price or other underlying value of transaction computed
       pursuant to Exchange Act Rule 0-11 (Set forth the amount on which the
       filing fee is calculated and state how it was determined):

    4) Proposed maximum aggregate value of transaction:

    5) Total fee paid:

[_] Fee paid previously with preliminary materials.

[_] Check box if any part of the fee is offset as provided by Exchange Act
    Rule 0-11(a)(2) and identify the filing for which the offsetting fee was
    paid previously. Identify the previous filing by registration statement
    number, or the Form or Schedule and the date of its filing.

    1) Amount Previously Paid:

    2) Form, Schedule or Registration Statement No.:

    3) Filing Party:

    4) Date Filed:
<PAGE>


                                AutoImmune Inc.

                   NOTICE OF ANNUAL MEETING OF SHAREHOLDERS

                          To Be Held on May 25, 2000

  The Annual Meeting of Shareholders of AutoImmune Inc. will be held on
Thursday, May 25, 2000 at 11:00 o'clock in the morning, Eastern Standard Time,
at the Louis D. Brandeis Conference Center, 16th Floor, Nutter, McClennen &
Fish, LLP, One International Place, Boston, Massachusetts, for the following
purposes:

    1. To elect a Board of Directors to serve for the ensuing year and until
       their successors are duly elected and qualified.

    2. To consider and act upon such other business and matters or proposals
       as may properly come before said Annual Meeting or any adjournment or
       adjournments thereof.

  The Board of Directors has fixed April 6, 2000 as the record date for
determining the shareholders having the right to receive notice of and to vote
at said Annual Meeting.

                                          By Order of the Board of Directors

                                          Constantine Alexander
                                          Secretary

Lexington, Massachusetts
April 13, 2000

  IF YOU DO NOT EXPECT TO BE PRESENT AT THIS MEETING AND WISH YOUR SHARES OF
CAPITAL STOCK TO BE VOTED, YOU ARE REQUESTED TO SIGN AND MAIL PROMPTLY THE
ENCLOSED PROXY WHICH IS BEING SOLICITED ON BEHALF OF THE BOARD OF DIRECTORS. A
RETURN ENVELOPE WHICH REQUIRES NO POSTAGE IF MAILED IN THE UNITED STATES IS
ENCLOSED FOR THAT PURPOSE.
<PAGE>

                                AUTOIMMUNE INC.

                                PROXY STATEMENT

                        ANNUAL MEETING OF SHAREHOLDERS
                                 May 25, 2000

  This proxy statement is furnished in connection with the solicitation by and
on behalf of the Board of Directors of AutoImmune Inc. of proxies for use at
AutoImmune's Annual Meeting of Shareholders to be held, pursuant to the
accompanying Notice of Annual Meeting, on Thursday, May 25, 2000, and at any
adjournment or adjournments thereof (the "Annual Meeting"). Action will be
taken at the Annual Meeting to elect a Board of Directors to serve for the
ensuing year and until their successors are duly elected and qualified.

  Shares of AutoImmune Inc. Common Stock, par value $0.01 per share,
represented by a properly executed proxy received and not revoked before the
Annual Meeting will be voted as directed in the proxy. If a proxy is signed
and returned, but does not specify how the shares represented the proxy are to
be voted, the proxy will be voted FOR the election of the nominees for
directors and in such manner as the proxies shall decide on any other matters
that may properly come before the Annual Meeting.

  AutoImmune's principal mailing address is located at 128 Spring Street,
Lexington, Massachusetts 02421. AutoImmune is mailing this proxy statement and
the related proxy on or about April 13, 2000 to its shareholders of record on
April 6, 2000.

                   ANNUAL REPORT AND INDEPENDENT ACCOUNTANTS

  AutoImmune's Annual Report to Shareholders for the fiscal year ended
December 31, 1999, including AutoImmune's financial statements and
PricewaterhouseCoopers LLP's report on the financial statements, is being
mailed with this proxy statement to each of AutoImmune's shareholders of
record on April 6, 2000. The Board of Directors has selected
PricewaterhouseCoopers as AutoImmune's independent accountants for the current
fiscal year. Representatives of PricewaterhouseCoopers are expected to be
present at the Annual Meeting where they will have the opportunity to make a
statement if they desire to do so and will be available to respond to
appropriate questions.

                               VOTING SECURITIES

  The holders of record of shares of Common Stock on April 6, 2000 may vote at
the Annual Meeting. On that date, there were 16,759,622 shares of Common Stock
outstanding and entitled to vote. Each share of Common Stock is entitled to
one vote on each matter listed in the Notice of Annual Meeting. If a quorum is
present at the Annual Meeting, the directors will be elected by a plurality of
the votes cast at the Annual Meeting by the holders of shares entitled to vote
at the Annual Meeting. Votes may be cast in favor of a nominee for director or
withheld. Votes that are withheld will have no effect on the outcome of the
election of directors.

  Any shareholder giving a proxy prior to the Annual Meeting has the power to
revoke it at any time before it is exercised by a written revocation received
by the Secretary of AutoImmune or by executing and returning a proxy bearing a
later date. Any shareholder of record attending the Annual Meeting may vote in
person, whether or not a proxy has been previously given, but the mere
presence of a shareholder at the Annual Meeting will not constitute revocation
of a previously given proxy. In addition, shareholders whose shares of Common
Stock are not registered in their own name will need additional documentation
from the record holder of such shares to vote personally at the Annual
Meeting.

<PAGE>

                             ELECTION OF DIRECTORS

  AutoImmune's By-Laws provide that the number of directors that shall
constitute the Board of Directors shall be determined by the Board of
Directors from time to time, but in no event shall the number of directors be
less than three. AutoImmune's Board of Directors has currently set the number
of directors at five.

  It is the intention of the persons named as proxies in the accompanying form
of proxy (unless authority to vote therefor is specifically withheld) to vote
for the election of the persons named in the following table, all of whom are
now directors of AutoImmune, to serve for the ensuing year and until their
successors are elected and qualified. In the event that any of the nominees
becomes unavailable (which is not now anticipated by AutoImmune), the persons
named as proxies have discretionary authority to vote for a substitute. The
Board of Directors has no reason to believe that any of said persons will be
unwilling or unable to serve if elected.

<TABLE>
<CAPTION>
                                                                      Director
                                  Name                            Age  Since
                                  ----                            --- --------
        <S>                                                       <C> <C>
        Robert C. Bishop, Ph.D...................................  57   1992
        Hugh A. D'Andrade........................................  61   1994
        Allan R. Ferguson........................................  57   1988
        R. John Fletcher.........................................  54   1991
        Henri A. Termeer.........................................  54   1992
</TABLE>

  Robert C. Bishop, Ph.D. has served as Chairman of the Board since May 1999
and as President and Chief Executive Officer of AutoImmune since he joined
AutoImmune in May 1992. Prior to joining AutoImmune, Dr. Bishop held senior
management positions at Allergan, Inc., an eye and skin care company,
including President, Allergan Medical Optics from 1986 to 1988, Senior Vice
President, Corporate Development from December 1988 to August 1989, President,
Allergan Pharmaceuticals, Inc. from August 1989 to February 1991 and Group
President, Therapeutics from February 1991 to May 1992. Dr. Bishop received
his B.A. degree and a Ph.D. in biochemistry from the University of Southern
California and his M.B.A. from the University of Miami. Dr. Bishop is also a
director of Quintiles Transnational Corp. and Millipore Corporation.

  Hugh A. D'Andrade has been Vice Chairman and Chief Administrative Officer of
Schering-Plough Corporation since January 1996 and was Executive Vice
President (Administration) of Schering-Plough Corporation from January 1984 to
January 1996. Mr. D'Andrade is also a director of Schering-Plough Corporation.

  Allan R. Ferguson has been Managing Director of 3i Technology Partners, an
international venture capital group, since July, 1999. From April 1993 to July
1999, Mr. Ferguson was General Partner of Atlas Venture, an international
venture capital fund which invests in early stage health care companies, and
leader of its Life Science team. He has also been a Managing Partner of Aspen
Venture Partners, L.P., a limited partnership formed to carry on the venture
capital activities of 3i Ventures in the United States, since March 1991. Mr.
Ferguson is also a director of FluidSense LLC.

  R. John Fletcher is the founder and Chief Executive Officer of Fletcher
Spaght, Inc., a management consulting firm, founded in 1983 specializing in
strategy development for high technology and health care businesses. Mr.
Fletcher is also a director of Nitinol Medical Technologies, Inc., MIJA
Industries, Inc. and Fisher Imaging Corp.

  Henri A. Termeer has been President since 1983, Chief Executive Officer
since 1985 and Chairman of the Board of Directors since 1988 of Genzyme
Corporation, an international health care company that develops, manufactures
and markets its own products. Mr. Termeer is also a director of ABIOMED, Inc.,
Genzyme Corp., Genzyme Transgenics Corp., Geltex Pharmaceuticals, Inc. and
Diacrin, Inc. Mr. Termeer is a Trustee of Hambrecht & Quist Healthcare
Investors, Inc. and Hambrecht & Quist Life Sciences, Inc., closed-end
investment companies whose investment advisor is Hambrecht & Quist Capital
Management Incorporated, an affiliate of Hambrecht & Quist LLC.

                                       2
<PAGE>

Committees of the Board of Directors

  The Board of Directors currently has formed the following committees:

    (a) Compensation Committee, consisting of Messrs. Ferguson, Fletcher and
  Termeer, the function of which is to review compensation paid to
  AutoImmune's officers and employees and to administer AutoImmune's stock
  option plans.

    (b) Audit Committee, consisting of Messrs. Ferguson, Fletcher and
  Termeer, the function of which is to consult with AutoImmune's independent
  auditors to ascertain compliance with appropriate audit procedures.

  During fiscal 1999, the Board of Directors met four times, the Audit
Committee met twice, and the Compensation Committee met twice. Each director
attended at least 75% of the aggregate of the meetings of the Board of
Directors and the meetings of the committees on which he served that were held
in fiscal year 1999 during the period that he served.

Certain Information Concerning the Board of Directors

  Directors currently do not receive any fees for service on the Board of
Directors but they are reimbursed for their expenses for each meeting
attended. In addition, pursuant to the Stock Option Plan for Nonemployee
Directors (the "Nonemployee Director Plan"), each director who is not an
employee of AutoImmune automatically receives an option to purchase 25,000
shares of Common Stock immediately following the annual meeting of
shareholders at which he is first elected and an option to purchase 6,500
shares of Common Stock annually thereafter if he continues to be eligible
under the terms of the Nonemployee Director Plan. Each nonemployee director
who is a member of any standing committee of the Board of Directors
automatically receives an additional option to purchase 1,000 shares of Common
Stock immediately following his first election to a standing committee of the
Board of Directors (a "Committee Initial Grant"). An option to purchase 1,000
shares of Common Stock is automatically granted every four years to a director
who continues to be a member of the standing committee for which he received a
Committee Initial Grant, provided that the director continues to be eligible
under the terms of the Nonemployee Director Plan. The exercise price of
options granted under the Nonemployee Director Plan is equal to the closing
price of a share of AutoImmune's Common Stock on the Nasdaq National Market
System on the date the option is granted. The options become exercisable in
four equal annual installments commencing one year after the date of grant,
provided that the director continues to be eligible under the terms of the
Nonemployee Director Plan.

  In addition, each nonemployee director is eligible to receive options to
purchase shares of Common Stock under the terms of AutoImmune's 1998 Stock
Option Plan. On February 18, 1999, each nonemployee director received an
option to purchase 10,000 shares of Common Stock under AutoImmune's 1998 Stock
Option Plan.

  All directors hold office until the next meeting of the shareholders of
AutoImmune and until their successors are elected and qualified. There are no
family relationships among directors or executive officers of AutoImmune.

Certain Relationships and Related Transactions

  John Fletcher, a director of AutoImmune, is the founder and Chief Executive
Officer of Fletcher Spaght, Inc., a management consulting firm. In September
1999, AutoImmune entered into an agreement with Fletcher Spaght under which
Fletcher Spaght evaluated the potential of AutoImmune's Colloral(R) product as
a nutraceutical and developed a strategy for launching that product. Fletcher
Spaght completed the services contemplated by the agreement prior to December
31, 1999. In consideration of these services, Fletcher Spaght received
$150,000 plus expenses.

  In January 2000, AutoImmune entered into a second agreement with Fletcher
Spaght under which Fletcher Spaght will continue to assist AutoImmune with the
potential launch of Colloral as a non-prescription

                                       3
<PAGE>

nutraceutical. In consideration of these services, Fletcher Spaght is entitled
to receive a monthly retainer of $10,000 starting in January 2000 and
continuing for five months. In addition, Fletcher Spaght is entitled to
receive a fee of (i) 5% of the amount, if any, that AutoImmune receives for
any or all U.S. rights to Colloral in a transaction consummated on or before
December 31, 2001 less (ii) the amount of retainer fees received by Fletcher
Spaght under the second agreement.

                            EXECUTIVE COMPENSATION

  The following table contains a summary of the annual, long-term and other
compensation for each of AutoImmune's fiscal years ended December 31, 1997,
1998 and 1999 of those persons who were, during 1999, the Chief Executive
Officer and every other person who served as an executive officer of
AutoImmune in 1999. AutoImmune did not grant any restricted stock awards or
stock appreciation rights or make any long term incentive plan payouts in
1999.

                          Summary Compensation Table

<TABLE>
<CAPTION>
                                                           Long Term
                                                          Compensation
                                                          ------------
                                                             Awards
                                                          ------------
                                   Annual Compensation     Securities
                                   ---------------------   Underlying      All Other
Name and Principal Position   Year Salary($)   Bonus($)    Options(#)   Compensation($)
- ----------------------------  ---- ----------  ---------  ------------  ---------------
<S>                           <C>  <C>         <C>        <C>           <C>
Robert C. Bishop.........     1997     306,538     73,600   216,000(2)       26,250(3)
 President and Chief          1998     328,154     98,500    25,000             --
  Executive Officer(1)        1999     352,750        --     20,000         477,885(4)

Heather A. Ellerkamp.....     1997      93,539     13,700    35,600(2)        8,500(3)
 Treasurer and Director       1998     107,192     10,500     9,000             --
  of Finance(5)               1999     107,971        --     87,000          83,308(4)

Jo Ann Wallace...........     1997     153,442     30,000   183,000(2)       14,333(7)
 Senior Vice President(6)     1998     174,769     43,750    15,000             620(8)
                              1999     187,822        --     12,000         210,865(4)
</TABLE>
- --------
(1) Dr. Bishop's full time employment by AutoImmune terminated on December 31,
    1999. He is still an executive officer of AutoImmune and continues to
    provide services to AutoImmune.
(2) Includes shares underlying options that were issued in replacement of
    options that were cancelled--199,000 for Dr. Bishop, 26,600 for Ms.
    Ellerkamp and 173,000 for Ms. Wallace.
(3) Represents an employee retention program payment equal to one month's
    salary.
(4) Represents a severance payment equal to 70 weeks base salary for Dr.
    Bishop, 38 weeks base salary for Ms. Ellerkamp and 51 weeks base salary
    for Ms. Wallace.
(5) Ms. Ellerkamp became an executive officer of AutoImmune on June 19, 1997.
    Ms. Ellerkamp's full time employment by AutoImmune terminated on November
    19, 1999. She is still an executive officer of AutoImmune and continues to
    provide services to AutoImmune.
(6)  Ms. Wallace left the employ of AutoImmune on October 29, 1999.
(7) Represents $1,000 in expenses for personal financial planning for which
    AutoImmune reimbursed Ms. Wallace and an employee retention program
    payment equal to one month's salary.
(8) Represents expenses for personal financial planning for which AutoImmune
    reimbursed Ms. Wallace.

                                       4
<PAGE>

                       OPTION GRANTS IN LAST FISCAL YEAR

  The following table sets forth information with respect to options granted
during fiscal year 1999 under AutoImmune's 1998 Stock Option Plan (the "1998
Plan") to the named executive officers.

<TABLE>
<CAPTION>
                                                                      Potential Realizable
                                     Percent of                         Value At Assumed
                         Number of  Total Options                     Annual Rates of Stock
                         Securities  Granted to                        Price Appreciation
                         Underlying   Employees                          for Option Term
                          Options     in Fiscal   Exercise Expiration ----------------------
      Name               Granted(#)    Year(1)    Price(2)    Date        5%        10%
      ----               ---------- ------------- -------- ---------- ---------- -----------
<S>                      <C>        <C>           <C>      <C>        <C>        <C>
Robert C. Bishop........   20,000        7.2%      $2.03     1/21/09  $   25,533    $64,706

Heather A. Ellerkamp....    7,000        2.5%       2.03     1/21/09       8,937     22,647
                           80,000       28.7%       0.53    11/18/09      26,665     67,575

Jo Ann Wallace..........   12,000        4.3%       2.03    10/29/00      15,320     38,824
</TABLE>
- --------
(1) Options to purchase a total of 278,500 shares were granted to employees in
    fiscal year 1999 under the Company's 1998 Plan.
(2) The exercise price may be paid in cash, by check or, in the discretion of
    the Committee, in shares of Common Stock valued at fair market value on
    the date of exercise or by delivery of a personal recourse note bearing
    interest payable not less than annually at no less than 100% of the lowest
    applicable Federal rate, as defined in Section 1274(d) of the Internal
    Revenue Code, or by any combination of the foregoing.

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

  The following table sets forth information as of December 31, 1999
concerning exercised and unexercised stock options held by the Chief Executive
Officer and the named executive officers.
<TABLE>
<CAPTION>
                                                                                      Value of Securities
                                                     Number of Securities           Underlying Unexercised
                                                    Underlying Unexercised          In-the-Money Options at
                           Shares                 Options at Fiscal Year End         Fiscal Year End($)(1)
                         Acquired on    Value     ------------------------------   -------------------------
      Name               Exercise(#) Realized($)  Exercisable     Unexercisable    Exercisable Unexercisable
      ----               ----------- -----------  -------------   --------------   ----------- -------------
<S>                      <C>         <C>          <C>             <C>              <C>         <C>
Robert C. Bishop........      --           --             694,000             --      $--             --
Heather A. Ellerkamp....      --           --              42,600          80,000      --         $22,400
Jo Ann Wallace..........   10,000      $16,900(2)         101,750             --       --             --
</TABLE>
- --------
(1) Based upon a fair market value of $0.81 for a share of AutoImmune's Common
    Stock which was the closing price for a share on December 31, 1999.
(2) Based upon a fair market value of $3.50 for a share of AutoImmune's Common
    Stock which was the closing price for a share on the date of exercise.

Consulting Arrangements

  Effective November 19, 1999 and December 31, 1999, Ms. Ellerkamp and Dr.
Bishop, respectively, ceased being employees of the Company and entered into
Consulting Agreements with the Company pursuant to which they agreed to
provide services similar to those they provided as employees, but on an hourly
basis. Under the Consulting Agreements, Dr. Bishop receives compensation of
$200 per hour for his services and Ms. Ellerkamp receives compensation of $100
per hour for her services.


                                       5
<PAGE>

            COMPENSATION COMMITTEE REPORT ON EXECUTIVE COMPENSATION

  The Compensation Committee of the Board of Directors is comprised of three
non-employee directors. The Committee is responsible for the establishment and
administration of AutoImmune's executive compensation program. In addition,
the Committee is responsible for the granting of awards under AutoImmune's
1998 Plan and for the administration of the AutoImmune's 1988 Stock Option
Plan, the 1998 Plan, the Nonemployee Director Plan and the AutoImmune Inc.
Employee Stock Purchase Plan.

  The Compensation Committee's basic policy in setting compensation for
AutoImmune's executive officers is to ensure that compensation is (a) designed
to align the interests of executive management with the long-term interests of
the shareholders and (b) competitive with the compensation paid by other
development stage biotechnology companies in order to attract and retain
executives. The Committee also endeavors to base compensation on each
individual's contribution to AutoImmune's success. The Committee's objective
is to have each executive's compensation package contingent on AutoImmune's
operational and, ultimately, financial success, as well as on individual
performance milestones. The Committee reviews the Chief Executive Officer's
performance and sets his compensation annually. Compensation recommendations
for AutoImmune's other executive officers are made by the Chief Executive
Officer and reviewed by the Compensation Committee.

  The cash compensation paid to each executive officer in fiscal year 1999 was
comprised solely of base salary. No incentive bonuses were paid. The Committee
believes that long term equity-based incentive compensation (in the form of
stock options) which is performance driven constitutes a fundamental element
of each executive officer's total compensation package. The Committee's policy
generally is that executive officers should have a compensation package that
places greater emphasis and dependence upon AutoImmune's success and stock
appreciation than on base salary.

  Base Salary. The base salary in fiscal year 1999 for each of the executive
officers, including the Chief Executive Officer, was established based on the
performance of the individual as well as on a review of the compensation paid
to persons holding comparable positions in other development stage
biotechnology companies. To determine the compensation paid by these
comparable companies, the Committee reviewed three published salary surveys.
Dr. Bishop's base salary had been set above the average paid to the chief
executive officers of comparable companies in recognition of Dr. Bishop's
extensive experience and because he joined AutoImmune at an early stage in its
development.

  In late 1999, the two remaining executive officers of AutoImmune, Dr. Bishop
and Ms. Ellerkamp, ceased being employees of the Company and became
consultants to the Company. As consultants, Dr. Bishop and Ms. Ellerkamp are
paid on an hourly basis at the rate of $200 per hour and $100 per hour,
respectively. The hourly rates are based on their most recent base salaries
and on rates charged currently by other consultants providing similar
services.

  Incentive Bonus. At the beginning of 1999, the compensation package included
a variable incentive bonus element of cash compensation. Due to the
unsuccessful results of the Phase III clinical trial of Colloral, however,
this element was eliminated for all officers.

  Stock Options. In fiscal 1999, the Committee recommended, and the Board of
Directors approved, grants of incentive stock options to the executive
officers which were designed to provide an incentive for these individuals to
work as a team to achieve the long term goals of AutoImmune.

                                          Respectfully submitted,

                                          Allan R. Ferguson
                                          R. John Fletcher
                                          Henri A. Termeer

                                       6
<PAGE>

               Comparison of Total Return Among AutoImmune Inc.,
                        NASDAQ Pharmaceutical Index and
                           the NASDAQ Composite Index

  The following graph compares, for the five year period commencing on December
31, 1994 and ending on December 31, 1999, the cumulative total return of
AutoImmune's Common Stock with the NASDAQ Pharmaceutical Index and the NASDAQ
Composite Index, assuming the investment of $100 on December 31, 1994.
AutoImmune has not paid any dividends on its Common Stock.

<TABLE>
<CAPTION>
                             31-Dec-94  31-Dec-95  31-Dec-96  31-Dec-97  31-Dec-98  31-Dec-99
                             ---------  ---------  ---------  ---------  ---------  ---------
<S>                          <C>        <C>        <C>        <C>        <C>        <C>
AutoImmune Inc.                 $100       $196       $267      $ 58       $ 39       $ 14
Nasdaq Pharmaceutical Index     $100       $183       $184      $190       $243       $451
Nasdaq Composite Index (U.S.)   $100       $141       $174      $214       $300       $543
</TABLE>

                                       7
<PAGE>

        SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT

  The following table sets forth certain information regarding the beneficial
ownership of AutoImmune's Common Stock as of March 8, 2000 by (i) those
persons known to AutoImmune to be the beneficial owners of more than five
percent of the outstanding shares of Common Stock of AutoImmune, (ii) each of
AutoImmune's directors, (iii) the executive officers named in the Summary
Compensation Table, and (iv) all directors and officers of AutoImmune as a
group. All information with respect to beneficial ownership by AutoImmune's
directors, officers or beneficial owners has been furnished by the respective
director, officer or beneficial owner, as the case may be. Where the number of
shares set forth below includes shares beneficially owned by spouses and minor
children, the named persons disclaim any beneficial interest in the shares so
included.

<TABLE>
<CAPTION>
                                                      Amount and
                                                      Nature of      Percent of
                                                      Beneficial       Common
Name and Address of Beneficial Owners                Ownership(1)      Stock
- -------------------------------------                ------------    ----------
<S>                                                  <C>             <C>
Five Percent or Greater Shareholders
Andrew H. Tisch and others(2).......................  1,632,000         9.74%
 667 Madison Avenue
 New York, NY 10021

State of Wisconsin Investment Board.................  1,590,000         9.49%
 P.O. Box 7842
 Madison, WI 53707

Biotechnology Value Fund LP(3)......................  2,312,709        13.80%
 227 West Monroe Street, Suite 4800
 Chicago, IL 60606

Directors
Robert C. Bishop....................................    753,339(4)      4.31%
Hugh A. D'Andrade...................................     98,750(5)         *
Allan R. Ferguson...................................     57,703(6)         *
R. John Fletcher....................................     36,060(7)         *
Henri A. Termeer....................................     49,750(8)         *

Named Executive Officers
Robert C. Bishop....................................    753,339(4)      4.31%
Heather Ellerkamp...................................     45,819(9)         *
Jo Ann Wallace......................................        --          0.00%

Directors and officers as a group (7 persons).......  1,041,421(10)     5.89%
</TABLE>
- --------
  * Less than 1%
 (1) Except as otherwise noted, each person referenced in the table has sole
     voting and investment power with respect to such person's shares.
 (2) Includes 408,000 shares of Common Stock held by Andrew H. Tisch, 408,000
     shares of Common Stock held by Daniel R. Tisch, 408,000 shares of Common
     Stock held by James S. Tisch, 408,000 shares of Common Stock held by
     Thomas J. Tisch. This information is provided pursuant to a Schedule 13G
     filed with the Securities and Exchange Commission on February 14, 2000.
 (3) Includes 936,609 shares of Common Stock held by Biotechnology Value Fund,
     L.P. and 1,304,550 shares of Common Stock held by Biotechnology Value
     Fund II, L.P. This information is provided pursuant to an Amendment to
     Schedule 13G filed with the Securities and Exchange Commission on
     February 11, 2000.
 (4) Includes 694,000 shares of Common Stock issuable upon the exercise of
     options that are exercisable within 60 days of the date of this table.

                                       8
<PAGE>

 (5) Includes 10,000 shares of Common Stock held by a trust of which Mr.
     D'Andrade is a trustee and 46,250 shares of Common Stock issuable upon
     the exercise of options that are exercisable within 60 days of the date
     of this table.
 (6) Includes 15,000 shares of Common Stock issuable to Aspen Venture
     Associates, L.P., the General Partner of Aspen Venture Partners, L.P.,
     upon the exercise of options, 12,403 shares of Common Stock owned by Mr.
     Ferguson, 24,250 shares of Common Stock that Mr. Ferguson has the right
     to acquire within 60 days of the date of this table pursuant to options,
     3,250 shares of Common Stock owned jointly by Mr. Ferguson and his
     spouse, 800 shares of Common Stock owned by Mr. Ferguson's spouse and
     2,000 shares of Common Stock owned by Mr. Ferguson as custodian for his
     children. Mr. Ferguson has shared voting and investment power with
     respect to all such shares of Common Stock except that Mr. Ferguson has
     sole voting and investment power with respect to the 12,403 shares of
     Common Stock owned by him and said 24,250 shares of Common Stock issuable
     upon the exercise of options and no voting and investment power with
     respect to the 800 shares held by his spouse. Mr. Ferguson disclaims
     beneficial ownership of the 800 shares of Common Stock owned by his
     spouse and the 2,000 shares of Common Stock owned by Mr. Ferguson as
     custodian for his children.
 (7) Includes 60 shares of Common Stock owned by Mr. Fletcher's minor children
     and 33,000 shares of Common Stock issuable upon the exercise of options
     that are exercisable within 60 days of the date of this table.
 (8) Includes 49,750 shares of Common Stock issuable upon the exercise of
     options that are exercisable within 60 days of the date of this table.
 (9) Includes 42,600 shares of Common Stock issuable upon the exercise of
     options that are exercisable within 60 days of the date of this table.
(10) Includes 904,850 shares of Common Stock issuable upon the exercise of
     options that are exercisable within 60 days of the date of this table by
     AutoImmune's current executive officers and directors.

                                       9
<PAGE>

                      SECTION 16(a) BENEFICIAL OWNERSHIP
                             REPORTING COMPLIANCE

  Section 16(a) of the Securities Exchange Act of 1934, as amended, requires
AutoImmune's directors, executive officers and persons who own more than ten
percent of a registered class of AutoImmune's equity securities to file with
the Securities and Exchange Commission initial reports of ownership and
reports of changes in ownership of Common Stock and other equity securities of
AutoImmune. Officers, directors and greater than ten percent beneficial owners
are required to furnish AutoImmune with copies of all Section 16(a) forms they
file.

  To AutoImmune's knowledge, based solely on review of the copies of such
reports furnished to AutoImmune and written representations that no other
reports were required, during the fiscal year ended December 31, 1999, all
Section 16(a) filing requirements applicable to AutoImmune's officers,
directors and greater than ten percent beneficial owners were satisfied,
except that grants of options to Robert Bishop and Heather Ellerkamp in
January 1999 were reported late on Form 5 and an amended Form 5, respectively.

                           PROPOSALS OF SHAREHOLDERS

  Proposals of shareholders intended to be presented at the next annual
meeting of shareholders must be received by AutoImmune at its principal
executive offices both (i) by December 15, 2000 if the proposal is to be
included in the proxy statement and form of proxy relating to that meeting and
(ii) within the time frames and in accordance with the procedures specified in
AutoImmune's By-laws and summarized below. The proposals also must comply with
the applicable requirements of the Federal securities laws.

  The By-laws of AutoImmune specify when a stockholder must submit proposals
(including nominees for election to the Board of Directors) for consideration
at a stockholders' meeting in order for those proposals to be considered at
the meeting. In order for a proposal to be considered at a stockholders'
meeting, the stockholder making it must have given timely notice in writing to
the Secretary of AutoImmune. To be timely, a stockholder's notice must be
delivered to or mailed and received at the principal mailing address of
AutoImmune, 128 Spring Street, Lexington, MA 02421, not less than 60 days nor
more than 90 days prior to the meeting; except that in the event that less
than 70 days' notice or prior public disclosure of the date of the meeting is
given or made to stockholders, notice by the stockholder to be timely must be
received no later than the close of business on the 10th day following the day
on which such notice of the date of the meeting was mailed or such public
disclosure was made.

                                      10
<PAGE>

                                 OTHER MATTERS

  The Board of Directors knows of no business which will be presented for
consideration at the Annual Meeting other than that shown above. However, if
any such other business should come before the Annual Meeting, it is the
intention of the persons named as proxies in the enclosed form of proxy to
vote the proxies in respect of any such business in accordance with their best
judgment.

  The cost of preparing, assembling and mailing this proxy material will be
borne by AutoImmune. AutoImmune may solicit proxies otherwise than by use of
the mail, in that certain officers and regular employees of AutoImmune,
without additional compensation, may use their personal efforts, by telephone
or otherwise, to obtain proxies. Such assistance may take the form of
personal, telephonic or written solicitation or any combination thereof. All
costs of solicitation will be borne by AutoImmune. AutoImmune will also
request persons, firms and corporations holding shares in their names, or in
the names of their nominees, which shares are beneficially owned by others, to
send this proxy material to and obtain proxies from such beneficial owners and
will reimburse such holders for their reasonable expenses in doing so.

                                          By Order of the Board of Directors

                                          Constantine Alexander
                                          Secretary

April 13, 2000

                                      11
<PAGE>



                                AUTOIMMUNE INC.

                 ANNUAL MEETING OF SHAREHOLDERS -- May 25, 2000

              Proxy Solicited On Behalf of the Board of Directors

  The undersigned shareholder hereby appoints Robert C. Bishop and Heather A.
Ellerkamp, and each of them individually, proxies for the undersigned, with
full power of substitution and re-substitution, to represent the undersigned
and to vote all shares of common stock of AUTOIMMUNE INC. (the "Company") that
the undersigned is entitled to vote at the Annual Meeting of Shareholders of
AutoImmune to be held on Thursday, May 25, 2000 and at any and all adjournments
thereof (the "Meeting"), as follows:

1. Election of Directors. Nominees:

         Robert C. Bishop, Ph.D.   Hugh A. D'Andrade   Allan R. Ferguson
                       R. John Fletcher   Henri A. Termeer

                  [_] FOR           [_] WITHHELD

FOR, except vote withheld for the following nominee(s), if any:

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

2.  Authorizing proxyholders to vote in their discretion as to such matters as
may properly come before the Meeting, other than proposals of which AutoImmune
has received proper notice in accordance with its By-laws.

  THE SHARES REPRESENTED BY THIS PROXY WILL BE VOTED AS DIRECTED HEREIN. IF NO
DIRECTION IS GIVEN, THIS PROXY WILL BE VOTED FOR ALL OF THE NOMINEES FOR
DIRECTOR AND SHALL BE DEEMED TO AUTHORIZE THE PROXYHOLDERS TO VOTE IN THEIR
DISCRETION AS TO ALL OTHER MATTERS THAT MAY PROPERLY COME BEFORE THE MEETING.

                             PLEASE SIGN ON REVERSE

<PAGE>



                                           ------------------------------------
                                           ------------------------------------
                                                       Signature(s)
                                           Dated: ______________________ , 2000

                                           NOTE: Please sign exactly as name
                                           or names appear above. When signing
                                           as Attorney, Executor, Trustee,
                                           Guardian, or Officer of a
                                           corporation, please give title as
                                           such. For joint accounts, all named
                                           holders should sign.

- --------------------------------------------------------------------------------
   PLEASE SIGN, DATE AND PROMPTLY RETURN THIS PROXY IN THE ENCLOSED ENVELOPE.



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