<PAGE>

                                  UNITED STATES

                       SECURITIES AND EXCHANGE COMMISSION

                             Washington, D.C. 20549

                                    FORM 10-Q

                                   (Mark One)

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

                  For the quarterly period ended March 31, 2002

                                       OR

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

                        Commission file number 000-30992

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

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


                              1020 Stony Hill Road
                              Yardley, Pennsylvania
                                      19067
                    ----------------------------------------
                    (Address of principal executive offices)
                                   (Zip Code)

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


                  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
                                                                   ---

As of May 10, 2002, 22,569,038 shares of common stock were outstanding.

<PAGE>

                       3-Dimensional Pharmaceuticals, Inc.

                                      Index

<TABLE>
<CAPTION>
                                                                          Page
                                                                          ----
<S>                                                                       <C>
Part I.    Financial Information

       Item 1.     Consolidated Financial Statements (unaudited)          3

                   Balance Sheets - - March 31, 2002 and
                   December 31, 2001                                      3

                   Statements of Operations - - Three months ended
                   March 31, 2002 and March 31, 2001                      4

                   Statements of Cash Flows - - Three months ended
                   March 31, 2002 and March 31, 2001                      5

                   Notes to Financial Statements                          6

       Item 2.     Management's Discussion and Analysis of
                   Financial Condition and Results of Operations          7-9

       Item 3.     Quantitative and Qualitative Disclosures
                   About Market Risk                                      10

 PART II.  Other Information                                              11

       Item 2.     Changes in Securities and Use of Proceeds              11

       Item 6.     Exhibits and Reports on Form 8-K.                      11

                   Signatures                                             12
</TABLE>

                                        2

<PAGE>

                         PART I - FINANCIAL INFORMATION

                          Item 1. Financial Statements.
                                   (Unaudited)

                       3-DIMENSIONAL PHARMACEUTICALS, INC.
                           CONSOLIDATED BALANCE SHEETS

<TABLE>
<CAPTION>
                                                                                March 31,       December 31,
                                                                                  2002              2001
                                                                              -------------    -------------
<S>                                                                           <C>              <C>
ASSETS
Current assets:
   Cash and cash equivalents ............................................     $  15,047,000    $  19,519,000
   Marketable securities ................................................        78,650,000       80,870,000
   Prepaid expenses and other current assets ............................         4,001,000        3,087,000
                                                                              -------------    -------------
     Total current assets ...............................................        97,698,000      103,476,000
Property and equipment, net .............................................        11,449,000       11,735,000
Restricted cash .........................................................           835,000          835,000
Other assets ............................................................           998,000        1,073,000
                                                                              -------------    -------------
                                                                              $ 110,980,000    $ 117,119,000
                                                                              =============    =============
LIABILITIES AND STOCKHOLDERS' EQUITY
Current liabilities:
   Accounts payable and accrued expenses ................................     $   2,848,000    $   5,759,000
   Current portion of deferred revenue ..................................        11,539,000        9,601,000
   Note payable .........................................................                 -        5,000,000
   Current portion of long-term debt ....................................         2,722,000        1,066,000
                                                                              -------------    -------------
     Total current liabilities ..........................................        17,109,000       21,426,000
Deferred revenue, less current portion ..................................         1,722,000        3,286,000
Long-term debt, less current portion ....................................         4,834,000          161,000
                                                                              -------------    -------------
                                                                                 23,665,000       24,873,000


COMMITMENTS AND CONTINGENCIES

STOCKHOLDERS' EQUITY
   Preferred stock--$.001 par value: 5,000,000 shares authorized,
       none issued and outstanding at March 31, 2002 and March 31, 2001                   -                -
   Common stock--$.001 par value: 45,000,000 shares authorized,
       22,503,103 and 21,988,238 shares issued and outstanding at
       March 31, 2002 and December 31, 2001 .............................            23,000           22,000
   Additional paid-in capital ...........................................       160,699,000      158,450,000
   Note receivable from officer .........................................          (260,000)        (260,000)
   Deferred compensation ................................................          (357,000)      (2,386,000)
   Accumulated deficit ..................................................       (73,490,000)     (64,703,000)
   Accumulated other comprehensive income ...............................           700,000        1,123,000
                                                                              -------------    -------------
Total stockholders' equity ..............................................        87,315,000       92,246,000
                                                                              -------------    -------------
                                                                              $ 110,980,000    $ 117,119,000
                                                                              =============    =============
</TABLE>

                                       3

<PAGE>


                      3-DIMENSIONAL PHARMACEUTICALS, INC.
                     CONSOLIDATED STATEMENTS OF OPERATIONS

<TABLE>
<CAPTION>
                                                                  Three months ended
                                                                       March 31,
                                                                 2002            2001
                                                              ------------    ------------
<S>                                                           <C>             <C>
Research and grant revenue ..............................     $  6,231,000    $  5,796,000

Costs and expenses:
       Research and development .........................        7,865,000       5,774,000
       Non-cash in-process research and development......        4,050,000               -
       General and administrative .......................        3,936,000       3,244,000
                                                              ------------    ------------
Total costs and expenses ................................       15,851,000       9,018,000
                                                              ------------    ------------
Loss from operations ....................................       (9,620,000)     (3,222,000)
Interest income .........................................          932,000       1,659,000
Interest expense ........................................          (99,000)        (78,000)
                                                              ------------    ------------
Net loss ................................................       (8,787,000)     (1,641,000)
                                                              ============    ============


Basic and diluted net loss per common share .............     $      (0.39)   $      (0.08)

Basic and diluted weighted average common
     shares outstanding .................................       22,357,000      21,313,000
                                                              ------------    ------------
</TABLE>



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

                                       4

<PAGE>

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

<TABLE>
<CAPTION>
                                                                 Three Months Ended March 31,
                                                                    2002             2001
                                                               --------------   --------------
<S>                                                            <C>              <C>
Cash flows from operating activities:
Net loss ...................................................   $  (8,787,000)   $  (1,641,000)
Adjustments to reconcile net loss to net cash provided by
   (used in) operating activities:
   Depreciation and amortization ...........................         983,000          551,000
   Amortization of premium on marketable securities ........         205,000          131,000
   Amortization of discount on marketable securities .......         (67,000)        (185,000)
   Accretion of interest on discounted note payable ........           5,000            8,000
   Acquisition of pre-clinical compound paid for with
     common stock ..........................................       4,050,000                -
   Non-cash compensation expense ...........................         172,000          256,000
   Valuation of options and warrants .......................          17,000                -
     Changes in:
       Other assets ........................................        (839,000)      (1,990,000)
       Accounts payable and accrued expenses ...............      (2,911,000)        (108,000)
       Settlement accrual ..................................               -         (500,000)
       Deferred revenue ....................................         374,000        3,684,000
                                                               -------------    -------------
            Net cash provided by (used in) operating
               activities ..................................      (6,798,000)         206,000
                                                               -------------    -------------

Cash flows from investing activities:
   Purchases of marketable securities ......................     (14,535,000)     (76,712,000)
   Sales and maturities of marketable securities ...........      16,194,000                -
   Cash restricted for collateral ..........................               -         (840,000)
   Capital expenditures ....................................        (697,000)        (836,000)
                                                               -------------    -------------
            Net cash provided by (used in) investing
               activities ..................................         962,000      (78,388,000)
                                                               -------------    -------------

Cash flows from financing activities:
   Proceeds from exercise of options and warrants ..........          40,000          250,000
   Repayment of short-term debt ............................      (5,000,000)               -
   Proceeds from issuance of long-term debt ................       6,502,000                -
   Repayment of long-term debt and notes payable ...........        (178,000)        (310,000)
                                                               -------------    -------------
            Net cash provided by financing
               activities ..................................       1,364,000          (60,000)
                                                               -------------    -------------

Net decrease in cash and cash equivalents ..................      (4,472,000)     (78,242,000)
Cash and cash equivalents-beginning of period ..............      19,519,000      114,557,000
                                                               -------------    -------------

Cash and cash equivalents-end of period ....................   $  15,047,000    $  36,315,000
                                                               =============    =============

Supplemental disclosures of cash flow information:
   Cash paid for interest ..................................   $      94,000    $      78,000
                                                               =============    =============
</TABLE>

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

                                       5

<PAGE>

3-DIMENSIONAL PHARMACEUTICALS, INC.
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(Unaudited)

1. Basis of Presentation

The unaudited consolidated financial statements included herein have been
prepared by the Company pursuant to the rules and regulations of the Securities
and Exchange Commission. Certain information and footnote disclosures normally
included in financial statements prepared in accordance with generally accepted
accounting principles have been condensed or omitted pursuant to such rules and
regulations. In management's opinion, the accompanying consolidated financial
statements contain all adjustments, consisting of normally recurring
adjustments, necessary for a fair presentation of the Company's financial
position and results of operations. Interim financial results are not
necessarily indicative of results anticipated for the full year. These unaudited
consolidated financial statements should be read in conjunction with the
Company's 2001 audited financial statements and footnotes included in the
Company's Annual Report on Form 10-K (File No. 000-30992).

The preparation of financial statements in conformity with generally accepted
accounting principles requires that management 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 amount of expenses incurred during the reporting period. Actual
results could differ from those estimates.

2. Net Loss Per Common Share

The Company has presented basic and diluted net loss per share pursuant to the
Statement of Financial Accounting Standards (SFAS) No. 128 Earnings per Share,
and the Securities and Exchange Commission's Staff Accounting Bulletin No. 98.
In accordance with SFAS 128, basic and diluted net loss per share has been
computed using the weighted-average number of shares of common stock outstanding
during the period, less shares subject to repurchase.

<TABLE>
<CAPTION>
                                                             Three Months Ended March 31,
                                                                 2002             2001
                                                                 ----             ----
<S>                                                          <C>              <C>
Net loss                                                     $ (8,787,000)    $ (1,641,000)
                                                             =============================
Basic and diluted net loss per share
   Weighted average shares of common stock outstanding         22,451,000       21,453,000
   Less: weighted average shares subject to repurchase            (94,000)        (140,000)
                                                             -----------------------------
   Weighted average shares used in computing basic and
     diluted net loss per share                                22,357,000       21,313,000
                                                             -----------------------------
   Basic and diluted net loss per share                      $      (0.39)    $      (0.08)
                                                             =============================
</TABLE>

The Company has excluded all stock options and warrants, and shares subject to
repurchase from the calculation of basic and diluted loss per common share
because all such securities are antidilutive for all applicable periods
presented.

3. Non-Cash In-Process Research and Development

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 recognized a non-cash in-process research and development
charge in the first quarter of 2002 of $4.1 million.

                                        6

<PAGE>

Item 2. Management's Discussion and Analysis of Financial Condition and Results
of Operations.

FORWARD-LOOKING STATEMENTS

This report includes "forward-looking statements" within the meaning of the safe
harbor provisions of the Private Securities Litigation Reform Act of 1995. These
forward-looking statements include, but are not limited to, statements about our
plans, objectives, representations and contentions and are not historical facts
and typically are identified by use of terms such as "may," "will," "should,"
"could," "expect," "plan," "anticipate," "believe," "estimate," "predict,"
"potential," "continue" and similar words, although some forward-looking
statements are expressed differently. You should be aware that the
forward-looking statements included herein represent management's current
judgment and expectations, but our actual results, events and performance could
differ materially from those in the forward-looking statements. The
forward-looking statements are subject to a number of risks and uncertainties,
including, but not limited to, risks associated with our new and uncertain
technologies, clinical trials and product development, the long and arduous
process of obtaining regulatory approval, our dependence on existing and new
strategic alliances, our dependence on patents and proprietary rights, our
ability to protect and enforce our patents and proprietary rights, the
development and availability of competitive products or technologies and our
ability to attract and retain talented employees and to manage our expansion as
a company increasingly focused on internal product research and development.
These risks and uncertainties are discussed in the section entitled "Factors
Affecting The Company's Prospects" of the Company's Annual Report on Form 10-K
for 2001 filed with the Securities and Exchange Commission. We do not intend to
update any of these factors or to publicly announce the results of any revisions
to these forward-looking statements at this time.

Overview

We are a small molecule drug discovery and development business that has a
pipeline of drug candidates in the areas of cancer, inflammation, and metabolic
and cardiovascular diseases. Until recently when we in-licensed a compound, all
of the drug candidates in our pipeline were discovered using all or a major
portion of our integrated set of proprietary technologies called
DiscoverWorks(R). We believe DiscoverWorks increases the productivity of the
drug discovery process by making it faster than traditional drug discovery
methods and by providing our scientists with the ability to design
characteristics into drug candidates that increase the probability of
development success. DiscoverWorks may also enable us to discover drugs that act
on many of the thousands of new drug targets revealed from sequencing the human
genome. We use DiscoverWorks to discover and develop drugs for our own pipeline
and in collaboration with pharmaceutical and biotechnology companies.

To date, substantially all of our revenue has been from corporate
collaborations, license agreements, and government grants. Revenue from
corporate collaborations and licensing agreements consists of up-front fees,
research and development funding, and milestone payments. Royalties from sales
of developed products are not expected for several years, if at all.

We have incurred substantial operating losses since our inception in 1993. As of
March 31, 2002, our accumulated deficit was $73.5 million. We have funded our
operations primarily through public and private placements of equity securities
totaling $153.0 million and cash received under collaborative agreements,
license agreements, and government grants of $74.2 million. Our losses have
resulted from costs incurred in research and development activities related to
technology development, internally funded drug discovery and development
programs, and associated administrative support costs. During 2001, we fulfilled
a significant portion of our near term staffing needs, increasing our staff from
125 to 200, including 90 Ph.D.s. The staff expansion has enabled us to increase
our DiscoverWorks capacity and initiate and advance our drug discovery programs.

Including first quarter revenue, 3DP's existing collaborations are expected to
provide revenue in 2002 of approximately $24 million, relating to up-front fees,
research funding payments and license fees. Not included in this estimate are
potential milestone payments from existing agreements or any revenue from
possible new collaborations. One of our goals is to enter into additional
DiscoverWorks collaborations.

Our ability to achieve profitability is dependent on the progress and
commercialization of drug candidates from existing programs and collaborations
and our ability to initiate and develop new programs and enter into additional
collaborations with favorable economic terms. Payments under drug discovery and
development agreements will be subject to significant fluctuation in both timing
and amount and therefore our results of operations for any period may not be
comparable to the results of operations for any other period.

                                       7

<PAGE>

Critical Accounting Policies

We believe our most critical accounting policy is 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. We estimate our performance period as the initial research term. The
actual performance period may vary. We will adjust the performance period
estimate based upon available facts and circumstances. Periodic payments for
research and development activities and government grants are recognized over
the period that we perform the related activities under the terms of the
agreements. Revenue resulting from the achievement of milestone events
stipulated in the agreements is recognized when we have (i) adequate evidence
that the milestone has been achieved and (ii) the achievement of the milestone
is deemed to be substantive. The determination whether the achievement of the
milestone is substantive is generally based upon the ability to verify the
developmental progress.

Results of Operations

Three Months Ended March 31, 2002 and 2001

Revenue. Our revenue for the three months ended March 31, 2002 was $6.2 million
as compared to $5.8 million for the three months ended March 31, 2001. The
revenue increase resulted from discovery collaborations with Johnson & Johnson
Pharmaceutical Research & Development, L.L.C., and an increase in research
funding from the Company's collaboration with Bristol-Myers Squibb Company,
which was partially off-set by the expiration of the research terms and related
funding of agreements with Dupont Pharmaceuticals Company and Aventis
CropScience GmbH.

Research and Development Expenses. Our research and development expenses
increased by $2.1 million, to $7.9 million for the three months ended March 31,
2002, compared to $5.8 million for the three months ended March 31, 2001. During
the quarter, we continued to expand our DiscoverWorks capacity and enhance our
investment in our drug discovery and development programs through increases in
personnel and facilities expenses.

Non-Cash In-Process Research and Development Expenses. We recorded a non-cash
in-process research and development expense of $4.1 million during the three
months ended March 31, 2002. The charge resulted from the issuance of 0.5
million shares of 3DP stock for the acquisition of worldwide rights to a pre-IND
compound from GSK for the prevention and treatment of thrombocytopenia, or low
blood platelet count. 3DP may issue up to 1.9 million additional shares of 3DP
stock if the compound achieves certain key development and regulatory milestone
events.

General and Administrative Expenses. Our general and administrative expenses
increased by $0.7 million to $3.9 million for the three months ended March 31,
2002, compared to $3.2 million for the three months ended March 31, 2001. The
increase was primarily related to increased management and personnel expenses,
increased investments in business development and facilities required to support
our research and development efforts, and other expenses relating to our
operations as a public company.

Other Income (Expenses). Interest income was $0.9 million for the three months
ended March 31, 2002 and $1.7 million for the three months ended March 31, 2001.
Interest income results from the investment of the proceeds from our initial
public offering and private placements of securities, as well as investment of
the up-front fees we have received from our collaborators. The decrease in
interest income is primarily attributable to the overall decrease in interest
rates and decreases in our cash balances.

Liquidity and Capital Resources

At March 31, 2002, we had cash, cash equivalents and marketable securities of
$93.7 million and working capital of $80.6 million. We have funded our
operations to date primarily through public and private placements of equity
securities with aggregate proceeds of approximately $153.0 million, and cash
received from corporate collaborations totaling $70.4 million, government grants
totaling $3.8 million, capital equipment and leasehold improvement financing
totaling $14.3 million and interest earned on our cash balances.

                                       8

<PAGE>

During the quarter, the Company repaid a $5.0 million short-term note and then
entered into a series of loans totaling $6.5 million, payable over 36 to 48
months, to finance the purchase of capital equipment and leasehold improvements.
There have been no other significant changes in the Company's contractual
obligations since year end.

To date, substantially all of our revenue has been from corporate
collaborations, license agreements and government grants. We expect that
substantially all of our revenue for the foreseeable future will come from
similar sources. We may incur increasing operating losses over the next several
years as we continue to fund internal product research and development and
further develop our technologies. We believe that our available cash and cash
equivalents, expected revenue from collaborations and license arrangements,
existing capital resources and interest income should be sufficient to fund
anticipated levels of operations for the next two years.

                                       9

<PAGE>

Item 3. Quantitative and Qualitative Disclosure About Market Risk

Our exposure to market risk for changes in interest rates relates primarily to
the increase or decrease in the amount of interest income we can earn on our
investment portfolio and on the increase or decrease in the amount of interest
expense we must pay with respect to our various outstanding debt instruments.
Our risk associated with fluctuating interest expense is limited to our capital
lease obligations, the underlying interest rates of which are closely tied to
market rates, and our investments in interest rate sensitive financial
instruments. Under our current policies, we do not use interest rate derivative
instruments to manage exposure to interest rate changes. We seek to ensure the
safety and preservation of our invested principal funds by limiting default
risk, market risk and reinvestment risk. We seek to minimize the risk of default
by investing in investment grade securities. A hypothetical 100 basis point
adverse move in interest rates along the entire interest rate yield curve would
not materially affect the fair value of our interest rate sensitive financial
instruments at March 31, 2002 or December 31, 2001. Declines in interest rates
over time will, however, reduce our interest income while increases in interest
rates over time will increase our interest expense.

                                       10

<PAGE>

                           PART II - OTHER INFORMATION

Item 2. Changes in Securities and Use of Proceeds

On January 7, 2002, the Company entered into a License Agreement with
GlaxoSmithKline Plc ("GSK") to acquire from GSK the worldwide rights to a
compound that the Company is now developing for the prevention and treatment of
thrombocytopenia, or low blood platelet count. Under the terms of the License
Agreement, the Company issued to GSK, in consideration for the world wide
rights, 500,000 shares of common stock and agreed to issue up to an additional
1.9 million shares of common stock to GSK depending upon whether the compound
achieves certain specified key development and regulatory milestones. The
Company's issuance of the 500,000 shares and agreement to issue, and any
issuance of, any or all of the 1.9 million additional shares of common stock are
exempt from registration under the Securities Act of 1933, as amended, based
upon Section 4(2) of that Act as a private placement of common stock.

Item 6. Exhibits and Reports on Form 8-K.

(a)  Exhibits.


None.

(b)  Reports on Form 8-K.


None.

                                       11

<PAGE>

        SIGNATURES

Pursuant to the requirements 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.

                3-Dimensional Pharmaceuticals, Inc.
                -----------------------------------
                (Registrant)

Date:  May 14, 2002         /s/ John M. Gill
       ------------         --------------------------------------------
                            John M. Gill
                            Chief Operating Officer (Principal Financial Officer
                            and Duly Authorized Signatory)



Date:  May 14, 2002         /s/ Scott M. Horvitz
       ------------         --------------------------------------------
                            Scott M. Horvitz
                            Vice President, Finance and Administration
                            (Principal Accounting Officer and
                            Duly Authorized Signatory)

                                       12

