<PAGE>

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                                 UNITED STATES
                      SECURITIES AND EXCHANGE COMMISSION
                            Washington, D.C. 20549

                              Amendment No. 2 to

                                   FORM 10-K

(Mark One)
 [X]         ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
                        SECURITIES EXCHANGE ACT OF 1934

                  For the fiscal year ended December 31, 2001

                                      OR

 [_]       TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
                        SECURITIES EXCHANGE ACT OF 1934

            For the transition period from __________to __________

                       Commission file number 000-30992

                      3-DIMENSIONAL PHARMACEUTICALS, INC.
            (Exact name of registrant as specified in its charter)

               Delaware                              23-2716487
       (State of incorporation)         (I.R.S. Employer Identification No.)


Three Lower Makefield Corporate Center, Suite 300, 1020 Stony Hill Road,
Yardley, PA 19067
               (Address of principal offices including zip code)

                                (267) 757-7200
              (Registrant's telephone number including area code)

          SECURITIES REGISTERED PURSUANT TO SECTION 12(b) OF THE ACT:

                                     None

          SECURITIES REGISTERED PURSUANT TO SECTION 12(g) OF THE ACT:

                                     None

  Indicate by check mark whether the registrant (1) has filed all reports
required to be filed by Section 13 or 15(d) of the Securities Exchange Act of
1934 during the preceding 12 months (or for such shorter period that the
registrant was required to file such reports), and (2) has been subject to
such filing requirements for the past 90 days. Yes [X] No [_]

  Indicate by check mark if disclosure of delinquent filers pursuant to Item
405 of Regulation S-K is not contained herein, and will not be contained, to
the best of registrant's knowledge, in the definitive proxy statement
incorporated by reference in Part III of this annual report on Form 10-K or
any amendment to this annual report on Form 10-K. [X]

   As of February 11, 2002, the aggregate market value of the Common Stock
held by non-affiliates of the registrant was $111,835,628. Such aggregate
market value was computed by reference to the closing sale price of the Common
Stock as reported on the Nasdaq National Market on such date.

  As of February 11, 2002, there were 22,494,902 shares of the registrant's
Common Stock outstanding.

                      DOCUMENTS INCORPORATED BY REFERENCE

  Portions of the definitive Proxy Statement for the Registrant's 2002 Annual
Meeting of Stockholders to be held on May 17, 2002, to be filed within 120
days after the end of the fiscal year covered by this Annual Report on Form
10-K, are incorporated by reference into Part III of this Report and certain
exhibits are incorporated by reference into Part IV of this Report.

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<PAGE>

Item 8. Financial Statements and Supplementary Data

                   INDEX TO CONSOLIDATED FINANCIAL STATEMENTS

                      3-DIMENSIONAL PHARMACEUTICALS, INC.

                                    CONTENTS
<TABLE>
<CAPTION>
                                                                          Page
                                                                          ----
<S>                                                                       <C>
Consolidated Financial Statements
 Report of independent public accountants
  As of and for the year ended December 31, 2001......................... F-2
  As of December 31, 2000 and for the years ended December 31, 2000 and
   1999.................................................................. F-3
Consolidated balance sheets as of December 31, 2001 and 2000............. F-4
Consolidated statements of operations for the years ended December 31,
 2001, 2000 and 1999..................................................... F-5
Consolidated statements of stockholders' equity (deficit) for the years
 ended December 31, 2001, 2000 and 1999.................................. F-6
Consolidated statements of cash flows for the years ended December 31,
 2001, 2000 and 1999..................................................... F-7
Notes to consolidated financial statements............................... F-8
</TABLE>
<PAGE>

                   REPORT OF INDEPENDENT PUBLIC ACCOUNTANTS

   To 3-Dimensional Pharmaceuticals, Inc.:

   We have audited the accompanying consolidated balance sheet of 3-
Dimensional Pharmaceuticals, Inc. (a Delaware corporation) and subsidiaries as
of December 31, 2001, and the related consolidated statements of operations,
stockholders' equity (deficit) and cash flows for the year then ended. These
financial statements are the responsibility of the Company's management. Our
responsibility is to express an opinion on these financial statements based on
our audit.

   We conducted our audit in accordance with auditing standards generally
accepted in the United States. Those standards require that we plan and
perform the audit to obtain reasonable assurance about whether the financial
statements are free of material misstatement. An audit includes examining, on
a test basis, evidence supporting the amounts and disclosures in the financial
statements. An audit also includes assessing the accounting principles used
and significant estimates made by management, as well as evaluating the
overall financial statement presentation. We believe that our audit provides a
reasonable basis for our opinion.

   In our opinion, the financial statements referred to above present fairly,
in all material respects, the financial position of 3-Dimensional
Pharmaceuticals, Inc. and subsidiaries as of December 31, 2001, and the
results of their operations and their cash flows for the year then ended in
conformity with accounting principles generally accepted in the United States.

                                             Arthur Andersen LLP

Philadelphia, Pennsylvania
February 19, 2002

                                      F-2
<PAGE>

INDEPENDENT AUDITORS' REPORT

Board of Directors and Stockholders
3-Dimensional Pharmaceuticals, Inc.
Yardley, Pennsylvania

   We have audited the accompanying consolidated balance sheet of 3-
Dimensional Pharmaceuticals, Inc. and subsidiary as of December 31, 2000 and
the related consolidated statements of operations, changes in stockholders'
equity (deficit) and cash flows for the years ended December 31, 2000 and
1999. These financial statements are the responsibility of the Company's
management. Our responsibility is to express an opinion on these financial
statements based on our audits.

   We conducted our audits in accordance with auditing standards generally
accepted in the United States of America. Those standards require that we plan
and perform the audit to obtain reasonable assurance about whether the
financial statements are free of material misstatement. An audit includes
examining, on a test basis, evidence supporting the amounts and disclosures in
the financial statements. An audit also includes assessing the accounting
principles used and significant estimates made by management, as well as
evaluating the overall financial statement presentation. We believe that our
audits provide a reasonable basis for our opinion.

   In our opinion, the financial statements referred to above present fairly,
in all material respects, the consolidated financial position of 3-Dimensional
Pharmaceuticals, Inc. and subsidiary as of December 31, 2000, and the
consolidated results of their operations and their cash flows for the years
ended December 31, 2000 and 1999 in conformity with accounting principles
generally accepted in the United States of America.

                                             Richard A. Eisner & Company, LLP

New York, New York
February 7, 2001

                                      F-3
<PAGE>

                      3-DIMENSIONAL PHARMACEUTICALS, INC.
                          CONSOLIDATED BALANCE SHEETS

<TABLE>
<CAPTION>
                                                    December 31,  December 31,
                                                    ------------  ------------
                                                        2001          2000
                                                    ------------  ------------
<S>                                                 <C>           <C>
                      ASSETS
Current assets:
 Cash and cash equivalents......................... $ 19,519,000  $114,557,000
 Marketable securities.............................   80,870,000           --
 Prepaid expenses and other current assets.........    3,087,000       977,000
                                                    ------------  ------------
   Total current assets............................  103,476,000   115,534,000
Property and equipment, net........................   11,735,000     5,508,000
Restricted cash....................................      835,000           --
Other assets.......................................    1,073,000     2,202,000
                                                    ------------  ------------
                                                    $117,119,000  $123,244,000
                                                    ============  ============
       LIABILITIES AND STOCKHOLDERS' EQUITY
Current liabilities:
 Accounts payable and accrued expenses............. $  5,759,000  $  3,193,000
 Current portion of deferred revenue...............    9,601,000     7,385,000
 Note payable......................................    5,000,000           --
 Current portion of long-term debt.................    1,066,000     1,209,000
 Current portion of settlement accrual.............          --        500,000
                                                    ------------  ------------
   Total current liabilities.......................   21,426,000    12,287,000
Deferred revenue, less current portion.............    3,286,000     9,619,000
Long-term debt, less current portion...............      161,000     1,315,000
                                                    ------------  ------------
                                                      24,873,000    23,221,000
                                                    ------------  ------------
COMMITMENTS AND CONTINGENCIES
STOCKHOLDERS' EQUITY
 Preferred Stock--$.001 par value: 5,000,000 shares
  authorized, none issued and outstanding at
  December 31, 2001 and 2000.......................           --            --
 Common stock--$.001 par value; 45,000,000 shares
  authorized, 21,988,238 and 21,385,798 shares
  issued and outstanding at December 31, 2001
  and December 31, 2000, respectively..............       22,000        21,000
 Additional paid-in capital........................  158,450,000   157,223,000
 Note receivable from officer......................     (260,000)     (390,000)
 Deferred compensation.............................   (2,386,000)   (3,570,000)
 Accumulated deficit...............................  (64,703,000)  (53,261,000)
 Accumulated other comprehensive income............    1,123,000           --
                                                    ------------  ------------
Total stockholders' equity.........................   92,246,000   100,023,000
                                                    ------------  ------------
                                                    $117,119,000  $123,244,000
                                                    ============  ============
</TABLE>

  The accompanying notes are an integral part of these consolidated financial
                                  statements.

                                      F-4
<PAGE>

                      3-DIMENSIONAL PHARMACEUTICALS, INC.
                     CONSOLIDATED STATEMENTS OF OPERATIONS

<TABLE>
<CAPTION>
                                              Year Ended December 31,
                                       ---------------------------------------
                                           2001         2000          1999
                                       ------------  -----------  ------------
<S>                                    <C>           <C>          <C>
Research and grant revenue...........  $ 28,399,000  $12,409,000  $  4,489,000
Costs and expenses:
 Research and development............    29,614,000   14,562,000    12,136,000
 General and administrative..........    15,334,000    8,652,000     6,525,000
 Litigation settlement...............           --           --      1,500,000
                                       ------------  -----------  ------------
                                         44,948,000   23,214,000    20,161,000
                                       ------------  -----------  ------------
Loss from operations.................   (16,549,000) (10,805,000)  (15,672,000)
Interest income......................     5,344,000    3,458,000       328,000
Interest expense.....................      (237,000)    (646,000)     (625,000)
                                       ------------  -----------  ------------
Loss before income taxes.............   (11,442,000)  (7,993,000)  (15,969,000)
Provision for income taxes...........           --       159,000           --
                                       ------------  -----------  ------------
Net loss.............................   (11,442,000)  (8,152,000)  (15,969,000)
Declared and accrued cumulative
 dividends on preferred stock........           --      (396,000)     (669,000)
                                       ------------  -----------  ------------
Net loss applicable to common stock..  $(11,442,000) $(8,548,000) $(16,638,000)
                                       ============  ===========  ============
Basic and diluted net loss per common
 share--historical...................  $      (0.53) $     (0.97) $     (27.37)
                                       ============  ===========  ============
Weighted average common shares
 outstanding--historical.............    21,626,000    8,778,000       608,000
                                       ============  ===========  ============
Basic and diluted net loss per common
 share--pro forma....................                $     (0.52) $      (1.57)
                                                     ===========  ============
Weighted average common shares
 outstanding--pro forma..............                 15,663,000    10,198,000
                                                     ===========  ============
</TABLE>


  The accompanying notes are an integral part of these consolidated financial
                                  statements.

                                      F-5
<PAGE>

                      3-DIMENSIONAL PHARMACEUTICALS, INC.
           CONSOLIDATED STATEMENTS OF STOCKHOLDERS' EQUITY (DEFICIT)
<TABLE>
<CAPTION>
                    Preferred Stock       Common Stock
                   ------------------  -------------------
                                                                           Notes                    Accumulated
                                                            Additional   Receivable                    Other
                                Par                  Par     Paid-in        From       Deferred    Comprehensive Accumulated
                     Shares    Value     Shares     Value    Capital      Officers   Compensation  Income (Loss)   Deficit
                   ----------  ------  ----------  ------- ------------  ----------  ------------  ------------- ------------
<S>                <C>         <C>     <C>         <C>     <C>           <C>         <C>           <C>           <C>
Balance--December
 31, 1998........   1,400,000  $1,000     733,979  $ 1,000 $  3,875,000  $(121,000)  $       --     $      --    $(29,140,000)
Common stock
 issued pursuant
 to exercise of
 stock options...         --      --       11,439      --        11,000        --            --            --             --
Value of options
 issued to
 consultants.....         --      --          --       --        18,000        --            --            --             --
Value of warrants
 issued in
 connection with
 bridge loan.....         --      --          --       --        26,000        --            --            --             --
Dividend declared
 on Series A-1
 preferred.......         --      --          --       --      (501,000)       --            --            --             --
Forgiveness of
 loans made to
 officers........         --      --          --       --           --      51,000           --            --             --
Net loss.........         --      --          --       --           --         --            --            --     (15,969,000)
                   ----------  ------  ----------  ------- ------------  ---------   -----------    ----------   ------------
Balance--December
 31, 1999........   1,400,000   1,000     745,418    1,000    3,429,000    (70,000)          --            --     (45,109,000)
Common stock
 issued pursuant
 to exercise of
 stock options,
 warrants and
 stock grants....         --      --      622,010      --     1,605,000   (521,000)          --            --             --
Common stock
 issued pursuant
 to cashless
 exercise of
 warrants........         --      --    1,017,230    1,000       (1,000)       --            --            --             --
Issuance of
 Series D
 preferred stock,
 net of offering
 costs of
 $24,000.........     625,000   1,000         --       --     4,976,000        --            --            --             --
Common stock
 issued pursuant
 to initial
 public offering,
 net of offering
 costs of
 $7,362,500......         --      --    5,750,000    6,000   78,882,000        --            --            --             --
Conversion of
 convertible
 preferred
 stock...........  (2,025,000) (2,000)    723,214    1,000        1,000        --            --            --             --
Conversion of
 redeemable
 preferred
 stock...........         --      --   12,463,389   12,000   63,523,000        --            --            --             --
Conversion of
 notes payable--
 dividends and
 accrued
 interest........         --      --       71,234      --     1,068,000        --            --            --             --
Dividends
 declared on
 Series A-1
 preferred.......         --      --          --       --      (563,000)       --            --            --             --
Value of options
 issued to
 consultants.....         --      --          --       --       392,000        --            --            --             --
Deferred
 compensation
 charge in
 connection with
 option grants...         --      --          --       --     3,983,000        --     (3,983,000)          --             --
Forfeiture of
 options subject
 to deferred
 compensation....         --      --          --       --       (53,000)       --         53,000           --             --
Deferred
 compensation
 expense.........         --      --          --       --           --         --        360,000           --             --
Common stock
 reacquired......         --      --       (6,697)     --       (19,000)    19,000           --            --             --
Forgiveness of
 loans made to
 officers........         --      --          --       --           --     182,000           --            --             --
Net loss.........         --      --          --       --           --         --            --            --      (8,152,000)
                   ----------  ------  ----------  ------- ------------  ---------   -----------    ----------   ------------
Balance--December
 31, 2000........         --      --   21,385,798   21,000  157,223,000   (390,000)   (3,570,000)          --     (53,261,000)
Common stock
 issued pursuant
 to exercise of
 stock options...         --      --      246,134      --       603,000        --            --            --             --
Common stock
 issued pursuant
 to exercise of
 warrants........         --      --      356,306    1,000       10,000        --            --            --             --
Value of options
 issued to
 consultants.....         --      --          --       --       433,000        --            --            --             --
Compensation
 charge in
 connection with
 acceleration of
 vesting terms on
 options.........         --      --          --       --       365,000        --            --            --             --
Forfeiture of
 options subject
 to deferred
 compensation....         --      --          --       --      (184,000)       --        184,000           --             --
Deferred
 compensation
 expense.........         --      --          --       --           --         --      1,000,000           --             --
Forgiveness of
 loans made to
 officer.........         --      --          --       --           --     130,000           --            --             --
Comprehensive
 loss:                                                                                                     --
 Net loss........         --      --          --       --           --         --            --                   (11,442,000)
 Unrealized gain
  on
  investments....         --      --          --       --           --         --            --      1,123,000            --
Comprehensive
 loss............
                   ----------  ------  ----------  ------- ------------  ---------   -----------    ----------   ------------
Balance--December
 31, 2001........         --   $  --   21,988,238  $22,000 $158,450,000  $(260,000)  $(2,386,000)   $1,123,000   $(64,703,000)
                   ==========  ======  ==========  ======= ============  =========   ===========    ==========   ============
<CAPTION>
                       Total
                   Stockholders'
                      Equity
                     (Deficit)
                   --------------
<S>                <C>
Balance--December
 31, 1998........  $(25,384,000)
Common stock
 issued pursuant
 to exercise of
 stock options...        11,000
Value of options
 issued to
 consultants.....        18,000
Value of warrants
 issued in
 connection with
 bridge loan.....        26,000
Dividend declared
 on Series A-1
 preferred.......      (501,000)
Forgiveness of
 loans made to
 officers........        51,000
Net loss.........   (15,969,000)
                   --------------
Balance--December
 31, 1999........   (41,748,000)
Common stock
 issued pursuant
 to exercise of
 stock options,
 warrants and
 stock grants....     1,084,000
Common stock
 issued pursuant
 to cashless
 exercise of
 warrants........           --
Issuance of
 Series D
 preferred stock,
 net of offering
 costs of
 $24,000.........     4,977,000
Common stock
 issued pursuant
 to initial
 public offering,
 net of offering
 costs of
 $7,362,500......    78,888,000
Conversion of
 convertible
 preferred
 stock...........           --
Conversion of
 redeemable
 preferred
 stock...........    63,535,000
Conversion of
 notes payable--
 dividends and
 accrued
 interest........     1,068,000
Dividends
 declared on
 Series A-1
 preferred.......      (563,000)
Value of options
 issued to
 consultants.....       392,000
Deferred
 compensation
 charge in
 connection with
 option grants...           --
Forfeiture of
 options subject
 to deferred
 compensation....           --
Deferred
 compensation
 expense.........       360,000
Common stock
 reacquired......           --
Forgiveness of
 loans made to
 officers........       182,000
Net loss.........    (8,152,000)
                   --------------
Balance--December
 31, 2000........   100,023,000
Common stock
 issued pursuant
 to exercise of
 stock options...       603,000
Common stock
 issued pursuant
 to exercise of
 warrants........        11,000
Value of options
 issued to
 consultants.....       433,000
Compensation
 charge in
 connection with
 acceleration of
 vesting terms on
 options.........       365,000
Forfeiture of
 options subject
 to deferred
 compensation....           --
Deferred
 compensation
 expense.........     1,000,000
Forgiveness of
 loans made to
 officer.........       130,000
Comprehensive
 loss:
 Net loss........   (11,442,000)
 Unrealized gain
  on
  investments....     1,123,000
                   --------------
Comprehensive
 loss............   (10,319,000)
                   --------------
Balance--December
 31, 2001........  $ 92,246,000
                   ==============
</TABLE>

  The accompanying notes are an integral part of these consolidated financial
                                  statements.

                                      F-6
<PAGE>

                      3-DIMENSIONAL PHARMACEUTICALS, INC.
                     CONSOLIDATED STATEMENTS OF CASH FLOWS

<TABLE>
<CAPTION>
                                              Year Ended December 31,
                                       ----------------------------------------
                                           2001          2000          1999
                                       ------------  ------------  ------------
<S>                                    <C>           <C>           <C>
Cash flows from operating activities:
Net loss.............................  $(11,442,000) $ (8,152,000) $(15,969,000)
Adjustments to reconcile net loss to
 net cash provided by (used in)
 operating activities:
 Depreciation and amortization.......     2,863,000     1,922,000     1,565,000
 Amortization of premium on
  marketable securities..............       851,000           --         19,000
 Amortization of discount on
  marketable securities..............      (691,000)          --            --
 Accretion of interest on discounted
  note payable.......................        34,000        26,000           --
 Non-cash compensation expense.......     1,495,000       201,000        51,000
 Valuation of options and warrants...       433,000       752,000        44,000
 Interest paid with common stock.....            --        49,000           --
 Interest paid with preferred stock..            --       239,000           --
  Changes in:
   Other assets......................      (981,000)   (1,899,000)      260,000
   Accounts payable and accrued
    expenses ........................     2,566,000       454,000     1,620,000
   Settlement accrual................      (500,000)   (1,000,000)    1,500,000
   Deferred revenue..................    (4,117,000)   16,116,000       345,000
                                       ------------  ------------  ------------
    Net cash provided by (used in)
     operating activities............    (9,489,000)    8,708,000   (10,565,000)
                                       ------------  ------------  ------------
Cash flows from investing activities:
 Purchases of marketable securities..  (137,978,000)          --            --
 Maturities of marketable
  securities.........................    58,071,000           --      7,267,000
 Cash restricted for collateral......       835,000           --            --
 Acquisition of subsidiary, net of
  $25,000 cash acquired..............           --            --         (5,000)
 Capital expenditures................    (9,090,000)   (3,469,000)     (278,000)
                                       ------------  ------------  ------------
    Net cash provided by (used in)
     investing activities............   (89,832,000)   (3,469,000)    6,984,000
                                       ------------  ------------  ------------
Cash flows from financing activities:
 Proceeds from sale of stock.........           --    102,212,000           --
 Proceeds from exercise of options
  and warrants ......................       614,000     1,068,000        11,000
 Dividends paid on Series A-1
  Preferred Stock....................           --       (229,000)          --
 Proceeds from issuance of short-term
  debt...............................     5,000,000           --     10,000,000
 Repayment of long-term debt and
  notes payable......................    (1,331,000)   (1,378,000)   (1,224,000)
                                       ------------  ------------  ------------
    Net cash provided by financing
     activities......................     4,283,000   101,673,000     8,787,000
                                       ------------  ------------  ------------
Net increase (decrease) in cash and
 cash equivalents....................   (95,038,000)  106,912,000     5,206,000
Cash and cash equivalents--beginning
 of year.............................   114,557,000     7,645,000     2,439,000
                                       ------------  ------------  ------------
Cash and cash equivalents--end of
 year................................  $ 19,519,000  $114,557,000  $  7,645,000
                                       ============  ============  ============
Supplemental disclosures of cash flow
 information:
 Cash paid for interest..............  $    204,000  $    331,000  $    446,000
 Noncash investing and financing
  activities:
  Equipment purchased under capital
   leases............................           --            --   $    390,000
  Dividends declared but not paid....                         --   $    501,000
  Note receivable exchanged for
   common stock......................           --   $    521,000           --
  Notes payable (including interest
   due of $89,000) exchanged for
   common stock......................           --   $  1,068,000           --
  Notes payable (including interest
   due of $353,000) exchanged for
   redeemable preferred stock........           --   $ 10,353,000           --
  Conversion of redeemable and
   convertible preferred stock to
   common stock......................           --   $ 71,751,000           --
</TABLE>

  The accompanying notes are an integral part of these consolidated financial
                                  statements.

                                      F-7
<PAGE>

                      3-DIMENSIONAL PHARMACEUTICALS, INC.

                         NOTES TO FINANCIAL STATEMENTS

                          December 31, 2001 and 2000

NOTE A--DESCRIPTION OF BUSINESS

   3-Dimensional Pharmaceuticals, Inc. (the Company) is a drug discovery and
development company that has a pipeline of drug candidates in the areas of
cancer and inflammation, and metabolic and cardiovascular diseases. The
Company has developed an integrated set of proprietary technologies called
DiscoverWorks(R) to accelerate and improve the drug discovery process.
DiscoverWorks enables scientists to design characteristics into drug
candidates that the Company believes increases the probability of development
success. The Company uses DiscoverWorks to discover and develop drugs for its
own pipeline and in collaboration with pharmaceutical and biotechnology
companies.

   The Company has incurred net losses since inception in 1993 and may incur
additional losses for at least the next several years. Through December 31,
2001, substantially all of the Company's revenue has been derived from
corporate collaborations, license agreements and government grants. The
Company expects that substantially all of its funds for the next several years
will result from payments from these sources, from outlicensing of
technologies and internally developed drug candidates, and from interest
income. The Company expects to spend significant resources to enhance its drug
discovery technologies and to fund research and development of its pipeline of
drug candidates. Through December 31, 2001, the Company's technologies have
not been used in the development of any compound that has reached the point of
commercialization. In order to achieve profitability, the Company must
continue to develop products and technologies that can be commercialized by
the Company or through existing and future collaborations.

NOTE B--SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES

 [1] Principles of consolidation:

   The consolidated financial statements include the accounts of the Company
and its wholly-owned subsidiaries. All inter-company balances have been
eliminated in consolidation.

 [2] Cash, cash equivalents and marketable securities:

   The Company considers all highly liquid investment instruments purchased
with an original maturity of three months or less to be cash equivalents.

   Marketable securities include investments in commerical paper, notes and
bonds with original maturities of greater than three months having a remaining
maturity of less than 24 months. These marketable securities are treated for
accounting purposes as available-for-sale and as such are reported at their
fair market values. At December 31, 2001, the Company had $1,123,000 of
unrealized gains on these marketable securities. All realized gains and losses
are recorded in the results of operations. Unrealized gains and losses have
been recorded as a separate component of stockholders' equity.

 [3] Restricted Cash:

   Restricted cash of $0.8 million at December 31, 2001 collateralizes a $0.8
million outstanding letter of credit associated with the lease of the
Company's Cranbury research facility. The funds are invested in a money market
fund. (Note K)

 [4] Property and equipment:

   Property and equipment are recorded at cost and depreciated using the
straight-line method over estimated useful lives of two to five years.
Leasehold improvements and equipment acquired under capital leases are
amortized over the lesser of the economic useful life of the improvement or
asset or the term of the lease. Expenditures for repairs and maintenance are
charged to expense as incurred, while major renewals and improvements are
capitalized.

                                      F-8
<PAGE>

                      3-DIMENSIONAL PHARMACEUTICALS, INC.

                         NOTES TO FINANCIAL STATEMENTS


 [5] Revenue recognition:

   Revenue from corporate collaborations and licensing agreements consists of
up-front fees, research and development funding and milestone payments. Non-
refundable up-front fees are deferred and amortized to revenue over the
related performance period. Periodic payments for research and development
activities and government grants are recognized over the period that the
Company performs the related activities under the terms of the agreements.
Revenue resulting from the achievement of milestone events stipulated in the
agreements is recognized when the milestone is achieved.

   In the year ended December 31, 1999, the Company changed its method of
recognizing revenue with respect to nonrefundable up-front fees received under
corporate collaboration research agreements to the method described above to
conform with the requirements of an accounting bulletin on revenue recognition
issued by the staff of the Securities and Exchange Commission in December 1999
and retroactively restated its prior years' financial statements to reflect
the application of the new method. Prior to the change, the Company recognized
revenue from such fees upon the execution of the agreement.

 [6] Research and development:

   Research and development costs are expensed as incurred.

 [7] Accounting for stock-based compensation:

   The Company accounts for its stock-based compensation plans under
Accounting Principles Board Opinion No. 25, "Accounting for Stock Issued to
Employees" (APB 25). In October 1995, the Financial Accounting Standards Board
issued Statement No. 123, "Accounting for Stock-Based Compensation" (SFAS No.
123), which establishes a fair value-based method of accounting for stock-
based compensation plans. The Company has adopted the disclosure-only
alternative under SFAS No. 123, which requires disclosure of the pro forma
effects on net loss and net loss per share as if stock-based employee
compensation was measured under SFAS No. 123, as well as certain other
information. The Company accounts for stock-based compensation to non-
employees using the fair value method in accordance with SFAS No. 123. The
Company has recognized deferred stock compensation related to certain stock
option grants (see Note I).

 [8] Use of estimates:

   The preparation of financial statements in conformity with generally
accepted accounting principles in the United States requires management to
make estimates and assumptions that affect the reported amounts of assets and
liabilities, the disclosure of contingent assets and liabilities at the date
of the financial statements, and the reported amounts of revenue and expenses
during the reporting period. Actual results could differ from those estimates.

 [9] Per share data:

   Historical basic and diluted net loss per common share is computed by
dividing the net loss increased by declared and accrued cumulative dividends
on the Series A-1 preferred stock for the year by the weighted average number
of common shares exclusive of outstanding shares of common stock which are
subject to repurchase and are nonvested. As their effects would be anti-
dilutive, shares of common stock issuable upon conversion of preferred stock
(for the periods prior to conversion) and exercise of outstanding options and
warrants as well as outstanding common shares which are nonvested during the
periods were not included in computing diluted net loss per common share.

                                      F-9
<PAGE>

                      3-DIMENSIONAL PHARMACEUTICALS, INC.

                         NOTES TO FINANCIAL STATEMENTS


   Securities and the related number of common shares not included in the
diluted computation for the years ended December 31, 2001, 2000 and 1999 that
could potentially dilute basic earnings per share, if any, in the future are
as follows:

                       Dilutive Potential Common Shares*

<TABLE>
<CAPTION>
                                                   2001       2000       1999
                                                 --------- ---------- ----------
   <S>                                           <C>       <C>        <C>
   Preferred Stock (see below)..................       --   6,858,000  9,545,000
   Options...................................... 2,991,000  2,115,000  2,023,000
   Warrants.....................................   279,000  1,531,000  1,843,000
   Common stock--subject to repurchase..........   111,000    179,000    115,000
                                                 --------- ---------- ----------
                                                 3,381,000 10,683,000 13,526,000
                                                 ========= ========== ==========
</TABLE>
  --------
   * Includes weighted average shares for period prior to conversion and
exercise.

   The preferred stock automatically converted into common stock on a 1 for
..36 basis and certain nonvested common stock automatically became vested upon
completion of the initial public offering of the Company's common stock in
August 2000. Accordingly, pro forma basic and diluted net loss per common
share on the accompanying consolidated statements of operations for the years
ended December 31, 2000 and 1999 has been calculated by dividing net loss by
the weighted average outstanding common shares as if the preferred stock were
converted into common stock, and certain nonvested common stock was vested, as
of the original date of issuance.

 [10] Comprehensive loss:

   Statement of Financial Accounting Standards No. 130, "Reporting
Comprehensive Income," requires the reporting of all changes in equity of an
enterprise that result from recognized transactions and other economic events
of the period other than transactions with owners in their capacity as owners.
The Company's other comprehensive loss includes unrealized gains on available
for sale securities.

 [11] Impairment of long-lived assets:

   As required by Statement of Financial Accounting Standards No.
121,"Accounting for the Impairment of Long-Lived Assets and for Long-Lived
Assets to be Disposed of," the Company assesses the recoverability of any
long-lived assets for which an indicator of impairment exists. Specifically,
the Company calculates, and recognizes, any impairment losses by comparing the
carrying value of these assets to its estimate of the undiscounted future
operating cash flows. Although its current and historical operating cash flows
are indicators of impairment, the Company believes that the future cash flows
to be received from its long-lived assets will exceed the assets' carrying
value. Accordingly, the Company has not recognized any impairment losses
through December 31, 2001.

 [12] Income taxes:

   The Company accounts for income taxes in accordance with Statement of
Financial Accounting Standards No. 109, "Accounting for Income Taxes." The
objective of this pronouncement is to recognize and measure, in accordance
with enacted tax laws, the amount of current and deferred income taxes payable
or refundable at the date of the financial statements as a result of all
events that have been recognized in the financial statements.


                                     F-10
<PAGE>

                      3-DIMENSIONAL PHARMACEUTICALS, INC.

                         NOTES TO FINANCIAL STATEMENTS


NOTE C--CERTAIN RESEARCH AND COLLABORATION AGREEMENTS

   In December 1997, the Company entered into a research collaboration with
Heska Corporation to assist in the discovery and development of new veterinary
therapeutic agents. The agreement originally had a two-year research term,
which was revived and extended until May 31, 2002. As of December 31, 2001,
the Company received up-front cash payments and research funding aggregating
approximately $2.7 million.

   In October 1999, the Company entered into a research collaboration and
license agreement with Hoechst Schering, AgrEvo GmbH, now part of Aventis
CropScience GmbH, under which the Company utilized its DirectedDiversity(R)
technology in the discovery of compounds applicable to plant and pest
management. The initial term of the agreement was for two years and was
extended until it expired in January 2002. As of December 31, 2001, the
Company has received up-front payments, payment for delivery of compounds and
research funding of approximately $3.4 million.

   In December 1999, the Company entered into a collaboration with Boehringer
Ingelheim Pharmaceuticals, Inc., or BIPI, to use its DirectedDiversity
technology to assist BIPI in the discovery of new drugs for specific
biological targets in humans. The initial term of the collaboration was for
two years and, in April 2001, the collaboration was expanded to cover
additional targets and the research term was extended until March 2003. As of
December 31, 2001, the Company has received up-front payments and research
funding aggregating approximately $4.1 million, and will receive additional
committed research funding of approximately $3.1 million over the remaining
term of the collaboration. The Company could also receive milestone payments
of up to $2.4 million for the first product developed depending on whether
stipulated milestones are met, and is eligible to receive additional milestone
payments if subsequent products are developed. The Company is also entitled to
receive royalties on the sales of resulting products.

   In February 2000, the Company entered into a collaboration with DuPont
Pharmaceuticals Company (acquired by Bristol-Myers Squibb Company in October
2001) under which the Company would utilize its DirectedDiversity technology
to develop new drugs for specific biological targets. As of December 31, 2001,
the Company has received up-front payments and research funding aggregating
approximately $2.6 million. The agreement expired on December 31, 2001, the
end of the initial research term of the collaboration.

   In March 2000, the Company was awarded and commenced a research project in
which it was the recipient of a two-year Small Business Innovative Research
(SBIR) award totaling up to $1 million. In addition, in June 2001, the Company
was awarded and commenced an additional research project under a two-year SBIR
Award totaling up to $1 million. The SBIRs are sponsored by the National
Institutes of Health.

   In May 2000, the Company entered into a license and research agreement with
Schering AG, Germany, in which Schering AG obtained, for human therapeutic
uses, exclusive worldwide rights to the Company's urokinase inhibitor
compounds. During the initial two-year research and development term, the
Company is to receive payments for research funding totaling $5 million, of
which $4.1 million was received by December 31, 2001. In addition, the Company
is eligible to receive milestone payments of up to approximately $23 million
for the first product developed in a therapeutic area depending on whether
stipulated milestones are met, and future milestone payments for additional
therapeutic areas and royalties on the sales of any resulting products. In
connection with the agreement, an affiliate of Schering AG made a $5 million
equity investment in the Company consisting of shares of preferred stock that
converted into 223,214 shares of common stock.

   In July 2000, the Company entered into a collaboration with Bristol-Myers
Squibb Company, or BMS, under which the Company will use its DiscoverWorks
technologies to assist BMS in the discovery and development of new human drugs
for specific biological targets. In the initial three-year term of the
research

                                     F-11
<PAGE>

                      3-DIMENSIONAL PHARMACEUTICALS, INC.

                         NOTES TO FINANCIAL STATEMENTS

collaboration, BMS will supply biological targets and the Company will create
chemical libraries and screen such libraries against these targets. BMS may
terminate research activities with 90 days notice, without cause, but must pay
any remaining research funding during the initial research term or one-half of
the remaining research funding during any extended term. Following the end of
the initial research or any extended research term, either party may terminate
the agreement on 30 days notice if no compound is being optimized or developed
under the collaborative agreement. The Company received up-front cash
licensing and technology access fees amounting to $19 million, net of a $4.5
million refund resulting from a modification of the agreement, and research
funding of $14.4 million has been committed over the first three years of the
collaboration of which $7.5 million was received by December 31, 2001.

   In addition, the Company could receive milestone payments through the
clinical development stages, and royalty payments on the sales of any
resulting products, with the amount at each level determined based on the
Company's involvement in the related optimization and development activities.
For each compound, depending on whether all pre-clinical and clinical
milestones are met and depending on the Company's contribution to the
development of the compound, the Company could receive milestone payments
aggregating up to between $4.5 million and $15 million.

   In December 2000, the Company entered into an agreement with Centocor,
Inc., a subsidiary of Johnson & Johnson, under which Centocor acquired
worldwide rights to the Company's direct thrombin inhibitor program. Centocor
is responsible for development and worldwide commercialization of all
compounds under the agreement. For the deep vein thrombosis indication, the
Company has an option to co-develop and co-promote with Centocor in the United
States. Under the agreement, the Company received an up-front cash payment of
$6 million from Centocor, research funding of $0.8 million during the year
ended December 31, 2001 and a milestone payment of $4 million in October 2001
and is eligible to receive additional committed research funding of $0.8
million over the remaining term of the contract. The Company could also
receive milestone payments of up to $38 million based on the achievement of
certain milestones for the first compound developed and approved under the
agreement. In addition, the Company is entitled to receive royalties on the
sales of any products marketed under the agreement.

   In December 2001, the Company entered into a collaboration with Johnson &
Johnson Pharmaceutical Research & Development, L.L.C., or J&J PRD, to utilize
the Company's DiscoverWorks technology to discover and optimize small molecule
drug leads directed towards genomics targets identified by J&J PRD. The
initial research term is for approximately one year, subject to renewal by
mutual agreement. Under the terms of this agreement, the Company received an
up-front technology access fee and committed research funding aggregating $3.6
million. The contract provides that the Company could also receive milestone
payments of up to $4.2 million for the first product developed depending on
whether stipulated milestones are met and could receive additional milestones
if subsequent products are developed. The contract also provides that the
Company is entitled to receive royalties on the sales of any resulting
products.

   All revenue from research and collaboration agreements is earned from
activities performed in the United States. Revenue from foreign corporate
collaborators (based on the location of the collaborator) comprised 13%, 30%
and 23% of total collaboration revenues for the years ended December 31, 2001,
2000 and 1999, respectively.

                                     F-12
<PAGE>

                      3-DIMENSIONAL PHARMACEUTICALS, INC.

                         NOTES TO FINANCIAL STATEMENTS


   Revenue from the Company's major customers as a percentage of total
revenue, for the years ended December 31, 2001, 2000 and 1999 was comprised of
the following:

<TABLE>
<CAPTION>
            Customer                     2001 2000 1999
            --------                     ---- ---- ----
            <S>                          <C>  <C>  <C>
            A........................... 43%  35%  --
            B........................... 30%  --   --
            C...........................  4%  16%   3%
            D...........................  9%  13%  --
            E...........................  8%  14%  --
            F........................... --   --   37%
            G........................... --    3%  27%
            H........................... --   --   20%
                                         ---  ---  ---
                                         94%  81%  87%
                                         ===  ===  ===
</TABLE>

   Deferred revenue at December 31, 2001, which consists of unamortized up-
front fees, is expected to be recognized as revenue in 2002 and 2003 in the
amounts of $9,601,000 and $3,286,000, respectively.

NOTE D--PROPERTY AND EQUIPMENT

   Property and equipment, all of which are located in the United States, is
summarized as follows:

<TABLE>
<CAPTION>
                                                      As of December 31,
                                                    ------------------------
                                                       2001         2000
                                                    -----------  -----------
      <S>                                           <C>          <C>
      Laboratory equipment, computer software and
       office equipment............................ $12,330,000  $ 6,720,000
      Leasehold improvements.......................   4,570,000    2,655,000
                                                    -----------  -----------
                                                     16,900,000    9,375,000
      Less accumulated depreciation and
       amortization................................  (5,165,000)  (3,867,000)
                                                    -----------  -----------
                                                    $11,735,000  $ 5,508,000
                                                    ===========  ===========
</TABLE>

NOTE E--ACCOUNTS PAYABLE AND ACCRUED EXPENSES

   Accounts payable and accrued expenses consist of the following:

<TABLE>
<CAPTION>
                                                           As of December 31,
                                                          ---------------------
                                                             2001       2000
                                                          ---------- ----------
      <S>                                                 <C>        <C>
      Professional fees.................................. $  950,000 $  289,000
      Equipment..........................................  1,473,000    685,000
      Payroll and related expenses.......................  1,615,000  1,280,000
      Trade payables.....................................  1,721,000    939,000
                                                          ---------- ----------
                                                          $5,759,000 $3,193,000
                                                          ========== ==========
</TABLE>

NOTE F--DEBT

 [1] Short-term note payable:

   On December 31, 2001, the Company completed a short-term note financing for
$5 million. The note bears interest at the prime rate of 4.75%. Principal and
interest is due by February 28, 2002. The Company intends to repay the
principal and interest and to arrange to refinance the amount borrowed as a
long-term note.

                                     F-13
<PAGE>

                      3-DIMENSIONAL PHARMACEUTICALS, INC.

                         NOTES TO FINANCIAL STATEMENTS


 [2] Convertible notes payable:

   On November 18, 1999, the Company completed a convertible note financing
for $10 million.

   The notes bore interest at the rate of prime + 1% per annum (9.5% through
December 31, 1999). Principal and interest was due on the first anniversary of
the closing date (the Maturity Date). The notes provided that, if prior to the
Maturity Date the Company raised an additional $10 million through the sale of
redeemable preferred stock, the notes and any unpaid accrued interest would
convert into the redeemable stock on the same terms and conditions as given to
the new investors. On March 31, 2000, the Company raised $18.4 million through
the sale of redeemable preferred stock, which upon completion of the IPO
converted into 2,186,101 shares of common stock. In connection therewith, the
$10 million of convertible notes and $353,000 of accrued interest were
converted into shares of redeemable preferred stock, which upon completion of
the IPO converted into 1,232,559 shares of common stock.

   In connection with the sale of the notes, the Company issued warrants to
purchase 1,250,000 shares of common stock exercisable at $3.50 per share for a
period of one year. The Company recorded a noncash interest charge in
connection with these warrants of $26,000 for the year ended December 31,
1999. All of the warrants were exercised prior to expiration, certain of which
on a net issuance basis, resulting in the issuance of 1,119,285 shares of
common stock.

 [3] Long-term debt:

   Long-term debt, including capital lease obligations, was as follows:

<TABLE>
<CAPTION>
                                                           As of December 31,
                                                          ---------------------
                                                             2001       2000
                                                          ---------- ----------
      <S>                                                 <C>        <C>
      Loans payable(a)................................... $1,010,000 $2,002,000
      Note payable(b)....................................    217,000    308,000
      Capital lease obligations..........................        --     214,000
                                                          ---------- ----------
                                                           1,227,000  2,524,000
      Current portion of long-term debt..................  1,066,000  1,209,000
                                                          ---------- ----------
      Long-term debt..................................... $  161,000 $1,315,000
                                                          ========== ==========
</TABLE>
--------
(a)  During 1998 and 1999, the Company entered into a series of 48-month loans
     to finance the purchase of laboratory equipment and office equipment and
     certain tenant improvements at interest rates varying between 10.68% and
     11.65%. The loans are payable in monthly installments of principal and
     interest aggregating $98,000 with final payments in 2002 and 2003
     aggregating $362,000 and $39,000, respectively. Borrowings related to the
     purchase of laboratory equipment and office equipment are collateralized
     by the equipment.
(b) The note is payable in annual installments of $125,000 through December
    2003. Interest on the note payable has been imputed at 10.0% per annum. As
    of December 31, 2001, the discounted amount of the note is $217,000 (face
    value $250,000).

   Minimum principal repayments of long-term debt as of December 31, 2001 were
as follows:

<TABLE>
      <S>                                                             <C>
      2002........................................................... $1,066,000
      2003...........................................................    161,000
                                                                      ----------
          Total...................................................... $1,227,000
                                                                      ==========
</TABLE>

                                     F-14
<PAGE>

                      3-DIMENSIONAL PHARMACEUTICALS, INC.

                         NOTES TO FINANCIAL STATEMENTS


NOTE G--FAIR VALUE OF FINANCIAL INSTRUMENTS

   Statement of Financial Accounting Standards No. 107, "Disclosures About
Fair Value of Financial Instruments," requires the Company to disclose the
estimated fair value of its financial instruments. The carrying amounts
reported in the balance sheets for cash and cash equivalents, accounts payable
and accrued expenses approximate fair value because of the short-term duration
of those items. The carrying amounts of debt and notes payable approximate
fair value because the interest rates on such debt approximate the market
rate.

NOTE H--REDEEMABLE PREFERRED STOCK AND EQUITY SECURITIES

 [1] Preferred stock:

   In August 2000, all outstanding Series A, B, C and D preferred shares and
the notes payable were automatically converted into common shares of the
Company on a 1 to .36 basis upon completion of the initial public offering of
the Company's common stock.

 [2] Common Stock:

   In August 2000, the Company completed an initial public offering of its
common stock. The offering consisted of 5,000,000 shares, which were priced at
$15 per share. The Company also granted its underwriters an option to purchase
750,000 shares to cover over allotments, which was exercised concurrently with
the IPO. Net proceeds to the Company after subtracting underwriting discounts
and expenses was $78,888,000.

 [3] Warrants:

   As of December 31, 2001, the Company has outstanding warrants to purchase
common shares, all of which are exercisable, as follows:

<TABLE>
<CAPTION>
                                      Expiration                         Number of Common
         Exercise Price                  Date                            Shares Reserved
         --------------               ----------                         ----------------
         <S>                          <C>                                <C>
             $0.03                       2005                                   5,894
             $0.03                       2006                                  90,599
             $0.03                       2007                                   5,336
             $7.00                       2004                                   4,500
                                                                             --------
                                                                             *106,329
                                                                             ========
</TABLE>
--------
* Weighted average exercise price was $.32 and weighted average remaining
contractual life was 4.44 years.

 [4] Common stock subject to repurchase:

   As of December 31, 2001 and 2000, 93,792 and 139,796 shares of common
stock, respectively, are subject to repurchase by the Company. The shares are
subject to repurchase at the Company's option at the original purchase prices,
ranging from $2.94 to $6.30, in the event that the purchaser's relationship
with the Company is terminated. The number of shares subject to repurchase by
the Company decreases by 25% on the one-year anniversary of the sale, and
further reduces upon later anniversary dates.

 [5] Note receivable from officer:

   At December 31, 2001, the Company has a note receivable from an officer
with an unpaid balance of $260,000 in connection with a loan made in March
2000 to purchase 176,871 restricted shares of the Company's common stock. The
loan is collateralized by the officer's beneficial interest in the stock.
Under the terms of the

                                     F-15
<PAGE>

                      3-DIMENSIONAL PHARMACEUTICALS, INC.

                         NOTES TO FINANCIAL STATEMENTS

note, interest accrues on the unpaid principal at approximately 7% per annum.
Principal and accrued interest is to be paid in four equal installments with
the first payment due six months from the loan date and the remaining payments
due annually thereafter. The Company has forgiven installments of principal
and interest due on loans to this officer and to other officers as part of the
overall executive compensation program. These amounts have been recorded as
compensation expense totaling $156,000, $182,000 and $58,000 for the years
ended December 31, 2001, 2000 and 1999, respectively.

NOTE I--EQUITY COMPENSATION PLANS

   The Company has maintained two equity compensation plans (together the
Plans) for the issuance of stock options and other stock grants to its
employees, non-employee directors, advisors and consultants.

   The Company's Equity Compensation Plan adopted in 1993, as amended,
provides for the issuance of restricted stock and the granting of both
incentive stock options and nonqualified stock options to purchase a total of
3,022,095 shares of common stock. The options vest over various periods, not
exceeding five years, and expire no later than ten years from date of grant.
Upon the close of the Company's IPO in August 2000, the Company stopped making
grants under the 1993 Plan.

   During 2000, the board of directors and stockholders approved the 2000
Equity Compensation Plan, which became effective upon the close of the IPO in
August 2000 and provided for the granting of up to 2,200,000 shares of common
stock. On May 14, 2001, the board of directors and stockholders increased the
number of shares under the plan to 4,200,000 shares of common stock.

   The 2000 Plan provides for grants of incentive stock options, nonqualified
stock options, stock awards and performance units.

   The Plans are administered by a committee of the board of directors. The
committee has the authority to determine the term during which an option may
be exercised (provided that no option may have a term of more than ten years),
the exercise price of an option and the rate at which options may be
exercised. Incentive stock options may be granted only to employees of the
Company. Nonqualified stock options may be granted to employees, directors or
consultants of the Company. For incentive stock options, the exercise price
may not be less than the fair value of the stock on the date of grant.

   The Company applies APB 25 in accounting for its employee stock option
awards, which requires the recognition of compensation expense for the
difference between the market value of the underlying common stock and the
exercise price of the option at the grant date.

   Pro forma information regarding net loss and loss per share is required by
SFAS No. 123, and has been determined as if the Company had accounted for its
employee stock options under the fair value method of that statement. The
weighted average fair value of options granted during the years ended December
31, 2001, 2000 and 1999 is estimated to be $6.80, $13.83 and $.35,
respectively. The fair value of these options was estimated at the date of
grant using the Black-Scholes option-pricing model with the following
assumptions:

<TABLE>
<CAPTION>
                                                      Year Ended December 31,
                                                      -------------------------
                                                       2001     2000     1999
                                                      -------  -------  -------
      <S>                                             <C>      <C>      <C>
      Risk-free interest rate........................     5.7%     5.9%     6.6%
      Expected life.................................. 6 Years  6 Years  6 Years
      Expected volatility............................     102%     120%      10%
      Divided yield..................................       0%       0%       0%
</TABLE>

                                     F-16
<PAGE>

                      3-DIMENSIONAL PHARMACEUTICALS, INC.

                         NOTES TO FINANCIAL STATEMENTS


   Had compensation cost for the Company's stock options been determined based
upon the fair value at the grant date for awards under the Plans consistent
with the methodology prescribed under SFAS No. 123, the Company's pro forma
net loss and pro forma net loss per share would be as follows:


<TABLE>
<CAPTION>
                                              Year Ended December 31,
                                        -------------------------------------
                                           2001         2000         1999
                                        -----------  -----------  -----------
   <S>                                  <C>          <C>          <C>
   Net loss:
    Historical......................... $11,442,000  $ 8,152,000  $15,969,000
    Pro forma..........................  15,652,000   10,388,000   16,398,000
   Basic and diluted net loss per
    share:
    Historical......................... $     (0.53) $     (0.97) $    (27.37)
    Pro forma.......................... $     (0.72) $     (1.23) $    (28.07)
</TABLE>

   The following table summarizes information about stock option activity
under the Plans during the periods indicated:

<TABLE>
<CAPTION>
                                   Incentive Options   Nonqualified Options
                                  -------------------- ------------------------
                                              Weighted               Weighted
                                              Average                Average
                                              Exercise              Excercise
                                    Shares     Price     Shares       Price
                                  ----------  -------- -----------  -----------
   <S>                            <C>         <C>      <C>          <C>
   Balance--December 31, 1998....  1,020,149   $ 2.08      160,487   $   1.92
   Granted.......................    157,585     2.94      727,619       3.67
   Exercised.....................    (11,439)    0.97           --         --
   Forfeited.....................    (31,541)    2.65           --         --
                                  ----------           -----------
   Balance--December 31, 1999....  1,134,754     2.20      888,106       3.35
   Granted.......................    455,170    11.07      431,090      15.17
   Exercised.....................   (200,569)    1.80     (191,433)      2.59
   Forfeited.....................   (133,832)    3.44           --         --
                                  ----------           -----------
   Balance--December 31, 2000....  1,255,523     5.34    1,127,763       8.00
   Granted.......................  1,096,421    10.16      230,142      12.66
   Exercised..................... (1,096,974)    2.45      (49,214)      2.44
   Forfeited.....................   (134,998)   10.46      (86,891)     15.17
                                  ----------           -----------
   Balance--December 31, 2001....  2,019,972   $ 7.90    1,221,800   $   8.59
                                  ----------   ------  -----------   --------
</TABLE>

   The following table presents information relating to stock options
outstanding and exercisable at December 31, 2001:

<TABLE>
<CAPTION>
                                 Options Outstanding       Options Exercisable
                            ------------------------------ --------------------
                                        Weighted
                                         Average  Weighted             Weighted
                                        Remaining Average              Average
                              Number      Life    Exercise   Number    Exercise
Range of Exercise Price     Outstanding in Years   Price   Exercisable  Price
-----------------------     ----------- --------- -------- ----------- --------
<S>                         <C>         <C>       <C>      <C>         <C>
Incentive Stock Options
  $0.03 to $7.28...........    904,494    6.77     $ 3.52    559,235    $ 2.45
  $7.29 to $30.00..........  1,115,478    9.20      11.44     48,690     16.02
                             ---------                       -------
                             2,019,972    8.11     $ 7.90    607,925    $ 3.54
                             =========             ======    =======    ======
Nonqualified Stock Options
  $0.03 to $7.28...........    710,853    7.40     $ 3.89    382,965    $ 3.66
  $7.29 to $30.00..........    510,947    8.98      15.14    109,503     17.54
                             ---------                       -------
                             1,221,800    8.06     $ 8.59    492,468    $ 6.75
                             =========             ======    =======    ======
</TABLE>

                                     F-17
<PAGE>

                      3-DIMENSIONAL PHARMACEUTICALS, INC.

                         NOTES TO FINANCIAL STATEMENTS


   In addition to the stock option activity, the Company issued 7,143 shares of
restricted stock at a weighted average purchase price per share of $6.30 under
the Plans during the year ended December 31, 2000. The Company reacquired 6,697
unvested, restricted shares at a purchase price of $19,000 during 2000.

   As of December 31, 2001, 2,689,242 common shares were available for future
grants under the 2000 Plan.

   The Company records expense for option grants to non-employees in the amount
of the fair value per share, as computed using the Black-Scholes option-pricing
model and variable plan accounting over the vesting period. The Company
recognized non-cash expense of $433,000, $392,000 and $18,000 for the years
ended December 31, 2001, 2000 and 1999, respectively in conjunction with such
non-employee option grants.

   During the year ended December 31, 2001, the Company recorded charges
totaling $365,000 resulting from changes in terms of certain stock options to
former employees, directors and consultants.

   During the year ended December 31, 2000, in connection with the grant of
options to employees and directors and the change in status of an option holder
from a consultant to an employee, the Company recorded deferred stock
compensation of $3,983,000, representing the difference between the exercise
price and the market value of the Company's common stock on the dates such
stock options were granted or status was changed. Deferred compensation is
included as a component of stockholders' equity (deficit) and is being
amortized to expense over the vesting period of the stock options. For the
years ended December 31, 2001 and 2000, the Company incurred deferred stock
compensation expense of $1,000,000 and $360,000, respectively.

NOTE J--401(K) PLAN

   The Company maintains a defined contribution 401(k) plan available to
eligible employees. Employee contributions are voluntary and are determined on
an individual basis, limited to the maximum amount allowable under federal tax
regulations. During the year ended December 31, 2001, the Company began making
matching contributions in the amount of 50% of employee contributions up to 6%.
The Company, at its discretion, may also make certain contributions to the
plan. For the years ended December 31, 2001 and 2000, the Company contributed
$266,000 as matching contributions and $226,000 as a discretionary contribution
to the plan, respectively. The Company made no contributions during 1999.

NOTE K--COMMITMENTS AND CONTINGENCIES

 [1] Leases:

   The Company currently occupies approximately 104,500 square feet of space,
including its corporate headquarters and clinical development offices in
Yardley, Pennsylvania and two research facilities located in Exton,
Pennsylvania and Cranbury, New Jersey. The Yardley facility includes 20,500
square feet of office space, which the Company occupied in October 2001 and
which is leased through March 2006. The Company leases approximately 41,000
square feet of space in Exton, Pennsylvania which houses one of the Company's
research and development facilities, including approximately 10,000 square
feet, adjacent to its initial space, which the Company occupied in December
2000. The initial 31,000 square feet of the Exton facility is leased through
June 2008 and the additional 10,000 square feet is subject to options allowing
the Company to extend that portion of the lease term through June 2008. The
Company's other research and development facility includes approximately 43,000
square feet of space in Cranbury, New Jersey. The Cranbury facility is leased
through May 2007. At December 31, 2001 minimum annual rentals under the leases
are as follows:

                                      F-18
<PAGE>

                      3-DIMENSIONAL PHARMACEUTICALS, INC.

                         NOTES TO FINANCIAL STATEMENTS


<TABLE>
<CAPTION>
         Year Ending December 31,                      Amount
         ------------------------                    -----------
         <S>                                         <C>
             2002................................... $ 2,418,000
             2003...................................   2,460,000
             2004...................................   2,503,000
             2005...................................   2,469,000
             2006...................................   2,412,000
           Thereafter...............................   1,207,000
                                                     -----------
                                                     $13,469,000
                                                     ===========
</TABLE>

   The leases provide for scheduled rental increases and escalations for
increases in real estate taxes and certain operating expenses. At December 31,
2001, the Company has recorded a deferred rent liability in the amount of
$84,000.

   Rent expense was $2,224,000, $547,000 and $516,000 for the years ended
December 31, 2001,2000 and 1999, respectively.

 [2] Letter of Credit:

   The Company had an outstanding letter of credit at December 31, 2001,
totaling $0.8 million pursuant to the lease for the Cranbury research
facility. (Note B[3])

 [3] Contingencies:

   The Company may be, from time to time, a party to various legal proceedings
arising from normal business activities. Although the amount of any liability
that could arise with respect to currently pending actions cannot be
accurately predicted, management believes that the ultimate resolution of
these matters will not have a material adverse effect on the Company's
financial condition or result of operations.

NOTE L--INCOME TAXES

   As of December 31, 2001, the Company has a net operating loss carryforward
and a research and development credit carryforward for federal income tax
purposes of approximately $49,680,000 and $2,909,000 respectively, which begin
to expire in 2016. In addition, the Company has an alternative minimum tax
credit carryforward of $120,000 as of December 31, 2001.

   Deferred tax assets, which represent the tax effects of loss and credit
carryforwards and temporary differences between the financial statement
amounts and the tax basis of assets and liabilities consist of:

<TABLE>
<CAPTION>
                                                        As of December 31,
                                                      ------------------------
                                                         2001         2000
                                                      -----------  -----------
   <S>                                                <C>          <C>
   Net operating loss carryforwards.................  $18,210,000  $14,760,000
   Research and development credit carryforwards....    2,909,000    1,321,000
   Alternative minimum tax credit carryforward......      120,000      117,000
   Income deferred for financial statement purposes,
    taxable when received for tax purposes..........    4,930,000    6,652,000
   Operating expenses, capitalized and amortized as
    start up costs for tax purposes.................          --       247,000
   Other--depreciation and expenses not currently
    deductible......................................      806,000      376,000
                                                      -----------  -----------
   Total deferred tax asset.........................   26,975,000   23,473,000
   Valuation allowance..............................  (26,975,000) (23,473,000)
                                                      -----------  -----------
       Net deferred tax asset.......................  $       --   $       --
                                                      ===========  ===========
</TABLE>

                                     F-19
<PAGE>

                      3-DIMENSIONAL PHARMACEUTICALS, INC.

                         NOTES TO FINANCIAL STATEMENTS


   The Company has not recorded a benefit from its carryforwards or deductible
temporary differences because realization of the benefit is uncertain and,
therefore, a valuation allowance has been provided for the deferred tax asset
at December 31, 2001 and 2000, respectively. The provision for income taxes
for the year ended December 31, 2000 represents a provision for the federal
alternative minimum tax and state income tax. The difference between the tax
benefit computed at the statutory tax rate of 34% and the Company's effective
tax rate is due to the increase in the valuation allowance of $3,502,000,
$4,305,000 and $6,805,000 for the years ended December 31, 2001, 2000 and
1999, respectively, and the provision for the federal alternative minimum tax
and state income tax of $159,000 for the year ended December 31, 2000. In
subsequent years, the Company may be subject to an annual limitation on the
utilization of its net operating loss and research and development tax credit
carryforwards under Section 382 of the Internal Revenue Code.

NOTE M--SETTLEMENT OF LITIGATION

   In October 1998, a complaint was filed in the United States District Court
for the District of Delaware by Anadys Pharmaceuticals, Inc. alleging that the
Company infringed two Anadys U.S. Patents. On March 7, 2000, the Company and
Anadys entered into a Settlement Agreement for a total of $1.5 million which
was paid by the Company for settlement of the litigation.

NOTE N--QUARTERLY RESULTS  (unaudited):

<TABLE>
<CAPTION>
                                          Quarter ended
                         --------------------------------------------------
                                                    September
                          March 31      June 30        30       December 31   Total Year
                         -----------  -----------  -----------  -----------  ------------
<S>                      <C>          <C>          <C>          <C>          <C>
          2001
Revenues................ $ 5,796,000  $ 6,643,000  $ 5,788,000  $10,172,000  $ 28,399,000
Net loss................  (1,641,000)  (3,094,000)  (4,965,000)  (1,742,000)  (11,442,000)
Basic net loss per
 common share--
 historical*............ $     (0.08) $     (0.14) $     (0.23) $     (0.08) $      (0.53)
Diluted net loss per
 common share--
 historical*............ $     (0.08) $     (0.14) $     (0.23) $     (0.08) $      (0.53)
                         ===========  ===========  ===========  ===========  ============
          2000
Revenues................ $ 1,484,000  $ 2,131,000  $ 4,994,000  $ 3,800,000  $ 12,409,000
Net income (loss).......  (3,742,000)  (2,477,000)     409,000   (2,342,000)   (8,152,000)
Basic net income (loss)
 per common share--
 historical*............ $     (5.92) $     (3.76) $      0.03  $     (0.11) $      (0.97)
Diluted net income
 (loss) per common
 share--historical*..... $     (5.92) $     (3.76) $      0.02  $     (0.11) $      (0.97)
Basic net income (loss)
 per common share--pro
 forma.................. $     (0.36) $     (0.18) $      0.02  $     (0.11) $      (0.52)
Diluted net income
 (loss) per common
 share--pro forma....... $     (0.36) $     (0.18) $      0.02  $     (0.11) $      (0.52)
                         ===========  ===========  ===========  ===========  ============
</TABLE>
--------
*  Per common share amounts for the quarters and full years have been
   calculated separately. Accordingly, quarterly amounts do not add to the
   annual amounts because of differences in the weighted average common shares
   outstanding during each period principally due to the effect of the
   Company's issuing shares of its common stock during the year.
(1) During the quarter ended December 31, 2000, revenues included a $0.4
    million adjustment resulting from a modification of the agreement with
    BMS.

                                     F-20
<PAGE>

NOTE O--TPO MIMETIC PROGRAM:

   In January 2002, the Company acquired worldwide rights to a pre-clinical
compound, 3DP-3534, from GlaxoSmithKline Plc, or GSK, for the prevention and
treatment of thrombocytopenia, or low blood platelet count. All payments for
the compound will be made to GSK in shares of the Company's stock. The Company
made an initial payment of 0.5 million shares and is obligated to issue up to
1.9 million additional shares should the compound achieve certain key
development and regulatory milestone events. With respect to the initial 0.5
million shares issued, the Company will recognize a non-cash in-process
research and development charge in the first quarter of 2002 of $4.1 million.

                                     F-21
<PAGE>

Item 9. Changes in and Disagreements with Accountants on Accounting and
Financial Disclosure

   On September 24, 2001, upon the recommendation of the Audit Committee and
the Board of Directors, the Company dismissed Richard A. Eisner & Company, LLP
(Eisner) as the Company's independent accountants. Eisner's reports on the
financial statements of the Company for each of the fiscal years ended
December 31, 2000 and 1999 did not contain an adverse opinion or a disclaimer
of opinion, and were not qualified or modified as to uncertainty, audit scope,
or accounting principles. During the Company's 2000 and 1999 fiscal years and
the interim period ended September 24, 2001, the Company did not have any
disagreements with Eisner on any matter relating to accounting principles or
practices, financial statement disclosure, or auditing scope or procedure,
which disagreements, if not resolved to the satisfaction of Eisner, would have
caused Eisner to make reference to the subject matter of the disagreement in
connection with its report.

   On September 24, 2001, the Board of Directors approved the Company's
retention of Arthur Andersen LLP to act as the Company's independent
accountants. During the Company's 2000 and 1999 fiscal years and the interim
period ended September 24, 2001, the Company did not consult Arthur Andersen
LLP regarding either the application of accounting principles to a specified
transaction, either completed or proposed, or the type of audit opinion that
might be rendered on the financial statements of the Company. Additionally,
the Company did not consult Arthur Andersen LLP during the Company's 2000 and
1999 fiscal years or the interim period ended September 24, 2001, regarding
any matter that was the subject of a disagreement or a reportable event.

                                   PART III

Item 10. Directors and Executive Officers of the Registrant

   The response to this item is contained in part under the caption "Executive
Officers of the Registrant" in Part I of this Annual Report on Form 10-K and
the remainder is incorporated by reference from the discussion under the
caption "Nomination and Election of Directors" from our Proxy Statement
relating to our Annual Meeting of Stockholders scheduled for May 17, 2002,
which will be filed within 120 days after the close of the Company's fiscal
year covered by this Report.

Item 11. Executive Compensation

   This information will be included in our Proxy Statement relating to our
Annual Meeting of Stockholders scheduled for May 17, 2002, which will be filed
within 120 days after the close of our fiscal year covered by this Report, and
is incorporated herein by reference to such Proxy Statement.

Item 12. Security Ownership of Certain Beneficial Owners and Management

   This information will be included in our Proxy Statement relating to our
Annual Meeting of Stockholders scheduled for May 17, 2002, which will be filed
within 120 days after the close of our fiscal year covered by this Report, and
is incorporated herein by reference to such Proxy Statement.

Item 13. Certain Relationships and Related Transactions

   This information will be included in our Proxy Statement relating to our
Annual Meeting of Stockholders scheduled for May 17, 2002, which will be filed
within 120 days after the close of our fiscal year covered by this Report, and
is incorporated herein by reference to such Proxy Statement.

                                     F-22
<PAGE>

                                    PART IV

Item 14. Exhibits, Financial Statement Schedules, and Reports on Form 8-K

     (a)  Documents filed as part of this report:

       (1)  Financial Statements

   The financial statements are included under Item 8 of this Report.

       (2)  Financial Statement Schedules

     The financial statement schedules listed under Item 8 of this Report are
  omitted because they are not applicable or required information, and are
  shown in the financial statements or the notes thereto.

       (3)  List of Exhibits.

   The following is a list of exhibits filed as part of this annual report on
Form 10-K. Where so indicated in parentheses, exhibits which were previously
filed are incorporated herein by reference.

<TABLE>
<CAPTION>
 Exhibit
 Number                                Description
 -------                               -----------
 <C>     <S>
  3 (i)  Ninth Restated Certificate of Incorporation of the Company
         (incorporated by reference to Exhibit 3.4 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606)).
  3 (ii) Amended and Restated Bylaws of the Company (incorporated by reference
         to Exhibit 3.5 to the Company's Registration Statement on Form S-1
         (File No. 333-37606)).
  4.1    Form of Common Stock Certificate of Company (incorporated by reference
         to Exhibit 4.1 to the Company's Registration Statement on Form S-1
         (File No. 333-37606)).
 10.1    3-Dimensional Pharmaceuticals, Inc. Equity Compensation Plan, as
         amended (incorporated by reference to Exhibit 10.1 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606))./1/
 10.2    Third Amended and Restated Stockholders' Agreement by and among the
         Company and the Stockholders identified therein, dated March 31, 2000
         (incorporated by reference to Exhibit 10.2 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606)).
 10.3    Series B Preferred Stock Purchase Agreement between the Company and
         Merck KGaA, dated October 11, 1996 (incorporated by reference to
         Exhibit 10.3 to the Company's Registration Statement on Form S-1 (File
         No. 333-37606)).
 10.4    Series C Preferred Stock Purchase Agreement between the Company and
         American Home Products Corporation, dated June 13, 1997 (incorporated
         by reference to Exhibit 10.4 to the Company's Registration Statement
         on Form S-1 (File No. 333-37606)).
 10.5    Series D Preferred Stock Purchase Agreement between the Company and
         Schering Berlin Venture Corporation, dated May 17, 2000 (incorporated
         by reference to Exhibit 10.5 to the Company's Registration Statement
         on Form S-1 (File No. 333-37606)).
 10.6    Warrant to Purchase Common Stock of the Company issued to HealthCare
         Ventures III, L.P., dated November 18, 1999 (incorporated by reference
         to Exhibit 10.6 to the Company's Registration Statement on Form S-1
         (File No. 333-37606)).
 10.7    Warrant to Purchase Common Stock of the Company issued to HealthCare
         Ventures IV, L.P., dated November 18, 1999 (incorporated by reference
         to Exhibit 10.7 to the Company's Registration Statement on Form S-1
         (File No. 333-37606)).
 10.8    Warrant to Purchase Common Stock of the Company issued to Rho
         Management Trust II, dated November 18, 1999 (incorporated by
         reference to Exhibit 10.8 to the Company's Registration Statement on
         Form S-1 (File No. 333-37606)).
</TABLE>


                                      F-23
<PAGE>

<TABLE>
<CAPTION>
 Exhibit
 Number                                Description
 -------                               -----------
 <C>     <S>
  10.9   Warrant to Purchase Common Stock of the Company issued to Aetna Life
         Insurance Company, dated November 18, 1999 (incorporated by reference
         to Exhibit 10.9 to the Company's Registration Statement on Form S-1
         (File No. 333-37606)).
  10.10  Warrant to Purchase Common Stock of the Company issued to Henry
         Rothman, dated November 18, 1999 (incorporated by reference to Exhibit
         10.10 to the Company's Registration Statement on Form S-1 (File No.
         333-37606)).
  10.11  Warrant to Purchase Common Stock of the Company issued to Abingworth
         Bioventures SICAV, dated November 18, 1999 (incorporated by reference
         to Exhibit 10.11 to the Company's Registration Statement on Form S-1
         (File No. 333-37606)).
  10.12  Warrant to Purchase Common Stock of the Company issued to Sentron
         Medical, Inc., dated November 18, 1999 (incorporated by reference to
         Exhibit 10.12 to the Company's Registration Statement on Form S-1
         (File No. 333-37606)).
  10.13  Warrant to Purchase Common Stock of the Company issued to Biotech
         Growth S.A., dated November 18, 1999 (incorporated by reference to
         Exhibit 10.13 to the Company's Registration Statement on Form S-1
         (File No. 333-37606)).
  10.14  Employment Offer Letter to David C. U'Prichard, dated September 1,
         1999 (incorporated by reference to Exhibit 10.14 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606))./1/
  10.15  Settlement Agreement between the Company and Anadys Pharmaceuticals,
         Inc. (Formerly Scriptgen Pharmaceuticals, Inc.), dated March 7, 2000
         (incorporated by reference to Exhibit 10.15 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606))./2/
  10.16  Research Collaboration Agreement between the Company and BioCryst
         Pharmaceuticals, Inc., dated October 18, 1996, and Amendment No.1
         thereto, dated October 18, 1996 (incorporated by reference to Exhibit
         10.16 to the Company's Registration Statement on Form S-1 (File No.
         333-37606))./2/
  10.17  Collaborative Discovery and Lead Optimization Agreement between the
         Company and Boehringer Ingelheim Pharmaceuticals, Inc., dated December
         17, 1999 (incorporated by reference to Exhibit 10.17 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606))./2/
  10.18  Collaborative Research and License Agreement between the Company and
         Hoechst Schering AgrEvo GmbH, now Aventis CropScience GmbH, dated
         October 18, 1999 (incorporated by reference to Exhibit 10.18 to the
         Company's Registration Statement on Form S-1 (File No. 333-37606))./2/
  10.19  Collaborative Research and License Agreement between the Company and
         E.I. DuPont de Nemours & Co., dated October 12, 1998 (incorporated by
         reference to Exhibit 10.19 to the Company's Registration Statement on
         Form S-1 (File No. 333-37606))./2/
  10.20  Collaborative Discovery and Lead Optimization Agreement between the
         Company and DuPont Pharmaceuticals Company, dated February 11, 2000
         (incorporated by reference to Exhibit 10.20 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606))./2/
  10.21  Nonexclusive Patent License Agreement between the Company and DuPont
         Pharmaceuticals Company, dated February 11, 2000 (incorporated by
         reference to Exhibit 10.21 to the Company's Registration Statement on
         Form S-1 (File No. 333-37606))./2/
  10.22  Research and License Agreement between the Company and the Heska
         Corporation, dated December 18, 1997, and Amendment No.1 thereto,
         dated December 18, 1997 (incorporated by reference to Exhibit 10.22 to
         the Company's Registration Statement on Form S-1 (File
         No. 333-37606))./2/
  10.23  License and Research Agreement between the Company and Schering AG,
         Germany, dated May 17, 2000 (incorporated by reference to Exhibit
         10.23 to the Company's Registration Statement on Form S-1 (File No.
         333-37606))./2/
</TABLE>


                                      F-24
<PAGE>

<TABLE>
<CAPTION>
 Exhibit
 Number                                Description
 -------                               -----------
 <C>     <S>
  10.24  Master Loan and Security Agreement between the Company and Phoenixcor,
         Inc., dated June 18, 1998 (incorporated by reference to Exhibit 10.24
         to the Company's Registration Statement on Form S-1 (File No. 333-
         37606)).
  10.25  Amended and Restated Lease for Combination Office/Laboratory/Light
         Manufacturing Space at Eagleview Corporate Center Lot 28 between the
         Company and Eagleview Technology Partners, dated December 12, 1997
         (incorporated by reference to Exhibit 10.25 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606)).
  10.26  Master Lease Agreement between the Company and Transamerica Business
         Credit Corporation, dated June 12, 1997 (incorporated by reference to
         Exhibit 10.26 to the Company's Registration Statement on Form S-1
         (File No. 333-37606)).
  10.27  Warrant to Purchase Common Stock of the Company issued to Transamerica
         Business Credit Corporation, dated June 12, 1997 (incorporated by
         reference to Exhibit 10.27 to the Company's Registration Statement on
         Form S-1 (File No. 333-37606)).
  10.28  Master Lease Agreement, Loan Agreement and Subordination Agreement
         between the Company and Comdisco, Inc., dated March 7, 1994
         (incorporated by reference to Exhibit 10.28 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606)).
  10.29  Warrant to Purchase Series A Preferred Stock, originally dated March
         7, 1994 and reissued to CDC Realty, Inc., dated July 21, 1998
         (incorporated by reference to Exhibit 10.29 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606)).
  10.30  Warrant to Purchase Series A Preferred Stock, originally dated March
         7, 1994 and reissued to Gregory Stento, dated July 21, 1998
         (incorporated by reference to Exhibit 10.30 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606)).
  10.31  Warrant to Purchase Series A Preferred Stock, originally dated April
         25, 1995 and reissued to Comdisco, Inc., dated July 21, 1998
         (incorporated by reference to Exhibit 10.31 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606)).
  10.32  Warrant to Purchase Series A Preferred Stock, originally dated April
         25, 1995 and reissued to Gregory Stento, dated July 21, 1998
         (incorporated by reference to Exhibit 10.32 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606)).
  10.33  Form of Warrant to Purchase Common Stock (along with Schedule of
         Holders of Certain Warrants to Purchase Common Stock) (incorporated by
         reference to Exhibit 10.33 to the Company's Registration Statement on
         Form S-1 (File No. 333-37606)).
  10.34  3-Dimensional Pharmaceuticals, Inc. 2000 Equity Compensation Plan
         (incorporated by reference to Exhibit 10.34 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606))./1/
  10.35  DiscoverWorks(TM) Drug Discovery Collaboration Agreement between the
         Company and Bristol-Myers Squibb Company, dated July 7, 2000
         (incorporated by reference to Exhibit 10.35 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606))./2/
  10.36  DiscoverWorks(TM) Nonexclusive License and Purchase Agreement between
         the Company and Bristol-Myers Squibb Company, dated July 7, 2000
         (incorporated by reference to Exhibit 10.36 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606))./2/
  10.37  Letter agreement between the Company and Bristol-Myers Squibb Company,
         dated December 18, 2000 (incorporated by reference to Exhibit 10.37 to
         the Company's Annual Report on Form 10-K (File No. 000-309992)).
  10.38  Research, Development and Commercialization Agreement between the
         Company and Centocor, Inc., dated as of December 29, 2000
         (incorporated by reference to Exhibit 10.38 to the Company's Annual
         Report on Form 10-K (File No. 000-30992))./2/
</TABLE>


                                      F-25
<PAGE>

<TABLE>
<CAPTION>
 Exhibit
 Number                                Description
 -------                               -----------
 <C>     <S>
  10.39  First Amendment to Lease between the Company and Eagleview Technology
         Partners dated October 24, 2000 (incorporated by reference to Exhibit
         10.39 to the Company's Annual Report on Form 10-K (File No. 000-
         30992))./2/
  10.40  Agreement of Sublease between the Company and Advanced Medicine, Inc.,
         dated December 13, 2000 (incorporated by reference to Exhibit 10.40 to
         the Company's Annual Report on Form 10-K (File No. 000-30992))./2/
  10.41  Additional and Alternative Target Agreement between the Company and
         Boehringer Ingelheim Pharmaceuticals, Inc. dated April 20, 2001
         (incorporated by reference to Exhibit 10.41 to the Company's Quarterly
         Report on Form 10-Q for the fiscal quarter period ended June 30, 2001
         (File No. 000-30992))./2/
  10.42  Amendment No. 1 dated May 16, 2001, to Discoverworks Drug Discovery
         Collaboration Agreement between the Company and Bristol-Myers Squibb
         Company, dated July 7, 2000 (incorporated by reference to Exhibit
         10.42 to the Company's Quarterly Report on Form 10-Q for the fiscal
         quarter period ended June 30, 2001 (File No. 000-30992))./2/
  10.43  Agreement of Lease dated June 14, 2001, between the Company and Cedar
         Brook Corporate Center, L.P. (incorporated by reference to Exhibit
         10.43 to the Company's Quarterly Report on Form 10-Q for the fiscal
         quarter period ended June 30, 2001 (File No. 000-30992)).
  10.44  Amendment No. 2 dated October 4, 2001, to Research, Development and
         Commercialization Agreement between the Company and Centocor, Inc.,
         dated December 29, 2000 (incorporated by reference to Exhibit 10.44 to
         the Company's Quarterly Report on Form 10-Q for the fiscal quarter
         period ended September 30, 2001 (File No. 000-30992))./2/
  10.45  Agreement of Lease dated August 8, 2002, between the Company and
         Newtown Office Development III, L.P. (incorporated by reference to
         Exhibit 10.45 to the Company's Quarterly Report on Form 10-Q for the
         fiscal quarter period ended September 30, 2001 (File No. 000-30992)).
  10.46  Collaboration Research and Development Agreement dated October 25,
         2001 between the Company and Athersys, Inc./4/,/5/.
  10.47  Discoverworks Drug Discovery Collaboration Agreement dated December
         28, 2001 between the Company and Janssen Pharmaceuticals and the R.W.
         Johnson Pharmaceutical Research Institute/4/,/5/.
  10.48  License Agreement dated January 7, 2002 between the Company and
         GlaxoSmithKline plc, including Exhibit D consisting of a Stock
         Purchase Agreement and a Registration Rights Agreement between the
         Company and GlaxoSmithKline plc./4/,/5/.
  11.1   Statements or computation of per share income (loss)./5/
  21.1   Subsidiaries of the Registrant (incorporated by reference to the
         Company's Annual Report on Form 10-K (File No. 000-30992)).
  23.1   Consent of Arthur Andersen LLP./3/
  23.2   Consent of Richard A. Eisner & Company, LLP./3/
  99.1   Letter relating to Arthur Andersen LLP./5/
</TABLE>

--------
/1/Compensation plans or arrangements in which directors and executive
   officers are eligible to participate.
/2/Confidential treatment granted with respect to portions of this exhibit.
   Omitted portions were filed separately with the Securities and Exchange
   Commission.
/3/Filed herewith.
/4/Confidential treatment has been requested with respect to portions of this
   exhibit. Omitted portions have been filed separately with the Securities
   and Exchange Commission.
/5/Previously filed.

     (b)  Reports on Form 8-K:

     None

                                     F-26
<PAGE>

                                  SIGNATURES

  Pursuant to the requirements of Section 13 or 15(d) of the Securities
Exchange Act of 1934, the Registrant has duly caused this Report to be signed
on its behalf by the undersigned, thereunto duly authorized.


Date: April 9, 2002                       3-Dimensional Pharmaceuticals, Inc.

                                                  /s/ Scott M. Horvitz
                                          By: _________________________________
                                              Scott M. Horvitz, Vice President
                                              Finance and Administration
                                              (Principal Accounting Officer)

<TABLE>
<CAPTION>
           Name                            Title                    Date
           ----                            -----                    ----
<S>                                   <C>                     <C>
       /s/ Scott M. Horvitz            Vice President,          April 9, 2002
-------------------------------------   Finance and
          Scott M. Horvitz              Administration
                                        (Principal
                                        Accounting Officer)
</TABLE>
<PAGE>

                               INDEX TO EXHIBITS

<TABLE>
<CAPTION>
 Exhibit
 Number                                Description
 -------                               -----------
 <S>     <C>
  3 (i)  Ninth Restated Certificate of Incorporation of the Company
         (incorporated by reference to Exhibit 3.4 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606)).
  3 (ii) Amended and Restated Bylaws of the Company (incorporated by reference
         to Exhibit 3.5 to the Company's Registration Statement on Form S-1
         (File No. 333-37606)).
  4.1    Form of Common Stock Certificate of Company (incorporated by reference
         to Exhibit 4.1 to the Company's Registration Statement on Form S-1
         (File No. 333-37606)).
 10.1    3-Dimensional Pharmaceuticals, Inc. Equity Compensation Plan, as
         amended (incorporated by reference to Exhibit 10.1 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606))./1/
 10.2    Third Amended and Restated Stockholders' Agreement by and among the
         Company and the Stockholders identified therein, dated March 31, 2000
         (incorporated by reference to Exhibit 10.2 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606)).
 10.3    Series B Preferred Stock Purchase Agreement between the Company and
         Merck KGaA, dated October 11, 1996 (incorporated by reference to
         Exhibit 10.3 to the Company's Registration Statement on Form S-1 (File
         No. 333-37606)).
 10.4    Series C Preferred Stock Purchase Agreement between the Company and
         American Home Products Corporation, dated June 13, 1997 (incorporated
         by reference to Exhibit 10.4 to the Company's Registration Statement
         on Form S-1 (File No. 333-37606)).
 10.5    Series D Preferred Stock Purchase Agreement between the Company and
         Schering Berlin Venture Corporation, dated May 17, 2000 (incorporated
         by reference to Exhibit 10.5 to the Company's Registration Statement
         on Form S-1 (File No. 333-37606)).
 10.6    Warrant to Purchase Common Stock of the Company issued to HealthCare
         Ventures III, L.P., dated November 18, 1999 (incorporated by reference
         to Exhibit 10.6 to the Company's Registration Statement on Form S-1
         (File No. 333-37606)).
 10.7    Warrant to Purchase Common Stock of the Company issued to HealthCare
         Ventures IV, L.P., dated November 18, 1999 (incorporated by reference
         to Exhibit 10.7 to the Company's Registration Statement on Form S-1
         (File No. 333-37606)).
 10.8    Warrant to Purchase Common Stock of the Company issued to Rho
         Management Trust II, dated November 18, 1999 (incorporated by
         reference to Exhibit 10.8 to the Company's Registration Statement on
         Form S-1 (File No. 333-37606)).
 10.9    Warrant to Purchase Common Stock of the Company issued to Aetna Life
         Insurance Company, dated November 18, 1999 (incorporated by reference
         to Exhibit 10.9 to the Company's Registration Statement on Form S-1
         (File No. 333-37606)).
 10.10   Warrant to Purchase Common Stock of the Company issued to Henry
         Rothman, dated November 18, 1999 (incorporated by reference to Exhibit
         10.10 to the Company's Registration Statement on Form S-1 (File No.
         333-37606)).
 10.11   Warrant to Purchase Common Stock of the Company issued to Abingworth
         Bioventures SICAV, dated November 18, 1999 (incorporated by reference
         to Exhibit 10.11 to the Company's Registration Statement on Form S-1
         (File No. 333-37606)).
 10.12   Warrant to Purchase Common Stock of the Company issued to Sentron
         Medical, Inc., dated November 18, 1999 (incorporated by reference to
         Exhibit 10.12 to the Company's Registration Statement on Form S-1
         (File No. 333-37606)).
</TABLE>

<PAGE>

<TABLE>
<CAPTION>
 Exhibit
 Number                                Description
 -------                               -----------
 <S>     <C>
  10.13  Warrant to Purchase Common Stock of the Company issued to Biotech
         Growth S.A., dated November 18, 1999 (incorporated by reference to
         Exhibit 10.13 to the Company's Registration Statement on Form S-1
         (File No. 333-37606)).
  10.14  Employment Offer Letter to David C. U'Prichard, dated September 1,
         1999 (incorporated by reference to Exhibit 10.14 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606))./1/
  10.15  Settlement Agreement between the Company and Anadys Pharmaceuticals,
         Inc. (Formerly Scriptgen Pharmaceuticals, Inc.), dated March 7, 2000
         (incorporated by reference to Exhibit 10.15 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606))./2/
  10.16  Research Collaboration Agreement between the Company and BioCryst
         Pharmaceuticals, Inc., dated October 18, 1996, and Amendment No.1
         thereto, dated October 18, 1996 (incorporated by reference to Exhibit
         10.16 to the Company's Registration Statement on Form S-1 (File No.
         333-37606))./2/
  10.17  Collaborative Discovery and Lead Optimization Agreement between the
         Company and Boehringer Ingelheim Pharmaceuticals, Inc., dated December
         17, 1999 (incorporated by reference to Exhibit 10.17 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606))./2/
  10.18  Collaborative Research and License Agreement between the Company and
         Hoechst Schering AgrEvo GmbH, now Aventis CropScience GmbH, dated
         October 18, 1999 (incorporated by reference to Exhibit 10.18 to the
         Company's Registration Statement on Form S-1 (File No. 333-37606))./2/
  10.19  Collaborative Research and License Agreement between the Company and
         E.I. DuPont de Nemours & Co., dated October 12, 1998 (incorporated by
         reference to Exhibit 10.19 to the Company's Registration Statement on
         Form S-1 (File No. 333-37606))./2/
  10.20  Collaborative Discovery and Lead Optimization Agreement between the
         Company and DuPont Pharmaceuticals Company, dated February 11, 2000
         (incorporated by reference to Exhibit 10.20 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606))./2/
  10.21  Nonexclusive Patent License Agreement between the Company and DuPont
         Pharmaceuticals Company, dated February 11, 2000 (incorporated by
         reference to Exhibit 10.21 to the Company's Registration Statement on
         Form S-1 (File No. 333-37606))./2/
  10.22  Research and License Agreement between the Company and the Heska
         Corporation, dated December 18, 1997, and Amendment No.1 thereto,
         dated December 18, 1997 (incorporated by reference to Exhibit 10.22 to
         the Company's Registration Statement on Form S-1 (File
         No. 333-37606))./2/
  10.23  License and Research Agreement between the Company and Schering AG,
         Germany, dated May 17, 2000 (incorporated by reference to Exhibit
         10.23 to the Company's Registration Statement on Form S-1 (File No.
         333-37606))./2/
  10.24  Master Loan and Security Agreement between the Company and Phoenixcor,
         Inc., dated June 18, 1998 (incorporated by reference to Exhibit 10.24
         to the Company's Registration Statement on Form S-1 (File No. 333-
         37606)).
  10.25  Amended and Restated Lease for Combination Office/Laboratory/Light
         Manufacturing Space at Eagleview Corporate Center Lot 28 between the
         Company and Eagleview Technology Partners, dated December 12, 1997
         (incorporated by reference to Exhibit 10.25 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606)).
  10.26  Master Lease Agreement between the Company and Transamerica Business
         Credit Corporation, dated June 12, 1997 (incorporated by reference to
         Exhibit 10.26 to the Company's Registration Statement on Form S-1
         (File No. 333-37606)).
  10.27  Warrant to Purchase Common Stock of the Company issued to Transamerica
         Business Credit Corporation, dated June 12, 1997 (incorporated by
         reference to Exhibit 10.27 to the Company's Registration Statement on
         Form S-1 (File No. 333-37606)).
</TABLE>
<PAGE>

<TABLE>
<CAPTION>
 Exhibit
 Number                                Description
 -------                               -----------
 <S>     <C>
  10.28  Master Lease Agreement, Loan Agreement and Subordination Agreement
         between the Company and Comdisco, Inc., dated March 7, 1994
         (incorporated by reference to Exhibit 10.28 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606)).
  10.29  Warrant to Purchase Series A Preferred Stock, originally dated March
         7, 1994 and reissued to CDC Realty, Inc., dated July 21, 1998
         (incorporated by reference to Exhibit 10.29 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606)).
  10.30  Warrant to Purchase Series A Preferred Stock, originally dated March
         7, 1994 and reissued to Gregory Stento, dated July 21, 1998
         (incorporated by reference to Exhibit 10.30 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606)).
  10.31  Warrant to Purchase Series A Preferred Stock, originally dated April
         25, 1995 and reissued to Comdisco, Inc., dated July 21, 1998
         (incorporated by reference to Exhibit 10.31 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606)).
  10.32  Warrant to Purchase Series A Preferred Stock, originally dated April
         25, 1995 and reissued to Gregory Stento, dated July 21, 1998
         (incorporated by reference to Exhibit 10.32 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606)).
  10.33  Form of Warrant to Purchase Common Stock (along with Schedule of
         Holders of Certain Warrants to Purchase Common Stock) (incorporated by
         reference to Exhibit 10.33 to the Company's Registration Statement on
         Form S-1 (File No. 333-37606)).
  10.34  3-Dimensional Pharmaceuticals, Inc. 2000 Equity Compensation Plan
         (incorporated by reference to Exhibit 10.34 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606))./1/
  10.35  DiscoverWorks(TM) Drug Discovery Collaboration Agreement between the
         Company and Bristol-Myers Squibb Company, dated July 7, 2000
         (incorporated by reference to Exhibit 10.35 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606))./2/
  10.36  DiscoverWorks(TM) Nonexclusive License and Purchase Agreement between
         the Company and Bristol-Myers Squibb Company, dated July 7, 2000
         (incorporated by reference to Exhibit 10.36 to the Company's
         Registration Statement on Form S-1 (File No. 333-37606))./2/
  10.37  Letter agreement between the Company and Bristol-Myers Squibb Company,
         dated December 18, 2000 (incorporated by reference to Exhibit 10.37 to
         the Company's Annual Report on Form 10-K (File No. 000-309992)).
  10.38  Research, Development and Commercialization Agreement between the
         Company and Centocor, Inc., dated as of December 29, 2000
         (incorporated by reference to Exhibit 10.38 to the Company's Annual
         Report on Form 10-K (File No. 000-30992))./2/
  10.39  First Amendment to Lease between the Company and Eagleview Technology
         Partners dated October 24, 2000 (incorporated by reference to Exhibit
         10.39 to the Company's Annual Report on Form 10-K (File No. 000-
         30992))./2/
  10.40  Agreement of Sublease between the Company and Advanced Medicine, Inc.,
         dated December 13, 2000 (incorporated by reference to Exhibit 10.40 to
         the Company's Annual Report on Form 10-K (File No. 000-30992))./2/
  10.41  Additional and Alternative Target Agreement between the Company and
         Boehringer Ingelheim Pharmaceuticals, Inc. dated April 20, 2001
         (incorporated by reference to Exhibit 10.41 to the Company's Quarterly
         Report on Form 10-Q for the fiscal quarter period ended June 30, 2001
         (File No. 000-30992))./2/
  10.42  Amendment No. 1 dated May 16, 2001, to Discoverworks Drug Discovery
         Collaboration Agreement between the Company and Bristol-Myers Squibb
         Company, dated July 7, 2000 (incorporated by reference to Exhibit
         10.42 to the Company's Quarterly Report on Form 10-Q for the fiscal
         quarter period ended June 30, 2001 (File No. 000-30992))./2/
</TABLE>
<PAGE>

<TABLE>
<CAPTION>
 Exhibit
 Number                                Description
 -------                               -----------
 <S>     <C>
  10.43  Agreement of Lease dated June 14, 2001, between the Company and Cedar
         Brook Corporate Center, L.P. (incorporated by reference to Exhibit
         10.43 to the Company's Quarterly Report on Form 10-Q for the fiscal
         quarter period ended June 30, 2001 (File No. 000-30992)).
  10.44  Amendment No. 2 dated October 4, 2001, to Research, Development and
         Commercialization Agreement between the Company and Centocor, Inc.,
         dated December 29, 2000 (incorporated by reference to Exhibit 10.44 to
         the Company's Quarterly Report on Form 10-Q for the fiscal quarter
         period ended September 30, 2001 (File No. 000-30992))./2/
  10.45  Agreement of Lease dated August 8, 2002, between the Company and
         Newtown Office Development III, L.P. (incorporated by reference to
         Exhibit 10.45 to the Company's Quarterly Report on Form 10-Q for the
         fiscal quarter period ended September 30, 2001 (File No. 000-30992)).
  10.46  Collaboration Research and Development Agreement dated October 25,
         2001 between the Company and Athersys, Inc./4/,/5/.
  10.47  Discoverworks Drug Discovery Collaboration Agreement dated December
         28, 2001 between the Company and Janssen Pharmaceuticals and the R.W.
         Johnson Pharmaceutical Research Institute/4/,/5/.
  10.48  License Agreement dated January 7, 2002 between the Company and
         GlaxoSmithKline plc, including Exhibit D consisting of a Stock
         Purchase Agreement and a Registration Rights Agreement between the
         Company and GlaxoSmithKline plc./4/,/5/.
  11.1   Statements or computation of per share income (loss)./5/
  21.1   Subsidiaries of the Registrant (incorporated by reference to the
         Company's Annual Report on Form 10-K (File No. 000-30992)).
  23.1   Consent of Arthur Andersen LLP./3/
  23.2   Consent of Richard A. Eisner & Company, LLP./3/
  99.1   Letter relating to Arthur Andersen LLP./5/
</TABLE>

--------
/1/Compensation plans or arrangements in which directors and executive
   officers are eligible to participate.
/2/Confidential treatment granted with respect to portions of this exhibit.
   Omitted portions were filed separately with the Securities and Exchange
   Commission.
/3/Filed herewith.
/4/Confidential treatment has been requested with respect to portions of this
   exhibit. Omitted portions have been filed separately with the Securities
   and Exchange Commission.
/5/ Previously filed.