<PAGE>   1

                                    FORM 10-Q

                       SECURITIES AND EXCHANGE COMMISSION
                              Washington, DC 20459

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

For the quarterly period ended March 31, 2000

[ ]    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 0-20713
                                                -------


                                 ENTREMED, INC.
                                 --------------
             (Exact name of registrant as specified in its charter)

            Delaware                                      58-1959440
            --------                                      ----------
(State or other jurisdiction of             (I.R.S. Employer Identification No.)
incorporation or organization)

                            9640 Medical Center Drive
                               Rockville, Maryland
                               -------------------
                    (Address of principal executive offices)

                                      20850
                                      -----
                                   (Zip code)

                                 (301) 217-9858
                                 --------------
              (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
    ---        ---

Indicate the number of shares outstanding of each of the issuer's classes of
common stock, as of the most recent practicable date.

           Class                                     Outstanding at May 9, 2000
------------------------------                      ----------------------------
Common Stock $.01 Par Value                                 15,297,609


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                                 ENTREMED, INC.


                                Table of Contents

PART I.   FINANCIAL INFORMATION                                PAGE
                                                               ----

Item 1 -- Financial Statements

Consolidated Balance Sheets
as of March 31, 2000 and December 31, 1999                      3

Consolidated Statements of
Operations for the Three Months Ended
March 31, 2000 and 1999                                         4

Consolidated Statements of Cash
Flows for the Three Months Ended March 31, 2000
and 1999                                                        5

Notes to Consolidated Financial
Statements                                                      6

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

Part II.  OTHER INFORMATION

Item 1 --      Legal Proceedings                               10

Item 2 --      Changes in Securities                           10

Item 3 --      Defaults upon Senior Securities                 10

Item 4 --      Submission of Matters to Vote of
               Security Holders                                10

Item 5 --      Other Information                               10

Item 6 --      Exhibits and Reports on Form 8-K                10

SIGNATURES                                                     11



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                                 ENTREMED, INC.
                           CONSOLIDATED BALANCE SHEETS

<TABLE>
<CAPTION>
                                                                                          March 31,              December 31,
                                                                                            2000                     1999
                                                                                     --------------------    --------------------
<S>                                                                                 <C>                     <C>
ASSETS                                                                                    (unaudited)
Current assets:
   Cash and cash equivalents                                                         $         29,328,842    $         26,027,235
   Interest receivable                                                                            130,017                 105,482
   Accounts receivable                                                                            700,378                 618,598
   Prepaid expenses and other                                                                     313,882                 336,443
                                                                                     --------------------    --------------------
Total current assets                                                                           30,473,119              27,087,758

Furniture and equipment, net                                                                    4,005,998               4,013,785

Other assets                                                                                      652,744                 742,082
                                                                                     --------------------    --------------------
      Total assets                                                                   $         35,131,861    $         31,843,625
                                                                                     ====================    ====================

LIABILITIES AND STOCKHOLDERS' EQUITY
Current liabilities:
   Accounts payable                                                                  $          3,505,212    $          4,887,693
   Accrued liabilities                                                                          1,084,884               1,756,538
   Deferred revenue                                                                                     -                  75,000
   Notes payable                                                                                  930,944               1,125,620
                                                                                     --------------------    --------------------
Total current liabilities                                                                       5,521,040               7,844,851

Note payable, less current portion                                                              1,754,525               1,995,327

Minority interest                                                                                  18,832                  18,646

Stockholders' equity:
   Convertible preferred stock, $1.00 par and $1.50
     Liquidation value:
     5,000,000 shares authorized, none issued and
     outstanding at March 31, 2000 (unaudited)
     and December 31, 1999                                                                              -                       -
   Common stock, $.01 par value:
     35,000,000 shares authorized, 15,449,060 (unaudited)
     and 14,755,998 shares issued and outstanding at
     March 31, 2000 and December 31, 1999, respectively                                           154,491                 147,560
   Treasury stock, at cost: 291,667 shares held
     March 31, 2000 (unaudited) and December 31, 1999                                          (3,833,379)             (3,833,379)
   Additional paid-in capital                                                                 124,350,659             107,863,638
   Accumulated deficit                                                                        (92,834,307)            (82,193,018)
                                                                                     --------------------    --------------------
Total stockholders' equity                                                                     27,837,464              21,984,801
                                                                                     --------------------    --------------------
      Total liabilities and stockholders' equity                                     $         35,131,861    $         31,843,625
                                                                                     ====================    ====================
</TABLE>

    The accompanying notes are an integral part of the financial statements.



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                                 ENTREMED, INC.
                      CONSOLIDATED STATEMENTS OF OPERATIONS
                                   (UNAUDITED)


<TABLE>
<CAPTION>
                                                               Three Months Ended
                                                                   March 31,
                                                            2000                1999
                                                       ---------------------------------

<S>                                                   <C>                  <C>
Revenues:
     Collaborative research and development            $         -          $  1,042,500
     Licensing                                                   -                50,000
     Grants                                                     92,507           158,819
     Royalties                                                 524,927           191,680
     Other                                                     109,265             1,040
                                                       ---------------      ------------

Total revenues                                                 726,699         1,444,039
                                                       ---------------      ------------


Costs and expenses:
     Research and development                                9,071,204         7,107,455
     General and administrative                              2,697,016         1,895,838
                                                       ---------------      ------------
                                                            11,768,220         9,003,293

Interest expense                                               (49,791)             -
Investment income                                              450,023           410,414
                                                       ---------------      ------------

Net loss                                               $   (10,641,289)     $ (7,148,840)
                                                       ===============      =============

Net loss per share (basic and diluted)                 $         (0.72)     $     ( 0.55)
                                                       ===============      =============

Weighted average number of shares
      outstanding (basic and diluted)                       14,831,911        13,057,561
                                                       ===============      =============
</TABLE>



    The accompanying notes are an integral part of the financial statements.



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                                 ENTREMED, INC.
                      CONSOLIDATED STATEMENTS OF CASH FLOWS
                                   (UNAUDITED)

<TABLE>
<CAPTION>
                                                                        Three Months Ended
                                                                             March 31,
                                                                   2000                   1999
                                                               -------------------------------------

<S>                                                            <C>                    <C>
CASH FLOWS FROM OPERATING ACTIVITIES
Net loss                                                        $(10,641,289)          $ (7,148,840)
Adjustments to reconcile net loss to net cash
     used by operating activities:
     Depreciation                                                    242,285                259,628
     Loss on equity investment                                        70,000                      -
     Loss on disposal of furniture and equipment                           -                 65,674
     Minority interest                                                   186                  9,465
     Changes in assets and liabilities:
        Accounts receivable                                          (81,780)              (190,396)
        Interest receivable                                          (24,535)               116,858
        Prepaid expenses and other                                    41,899                102,127
        Accounts payable                                          (1,382,481)             1,232,054
        Accrued liabilities                                         (671,654)              (201,792)
        Deferred revenue                                             (75,000)            (1,092,501)
                                                                ------------           ------------
      Net cash used by operating activities                      (12,522,369)            (6,847,723)
                                                                ------------           ------------

CASH FLOWS FROM INVESTING ACTIVITIES
Maturities of short-term investments                                       -              2,845,556
Purchases of furniture and equipment                                (234,498)              (933,060)
                                                                ------------           ------------
      Net cash (used) provided by investing activities              (234,498)             1,912,496
                                                                ------------           ------------

CASH FLOWS FROM FINANCING ACTIVITIES
Proceeds from option and warrant exercises                        16,493,952                207,351
Payment of note payable                                             (435,478)                     -
                                                                ------------           ------------
      Net cash provided by financing activities                   16,058,474                207,351
                                                                ------------           ------------

Net increase (decrease) in cash and cash equivalents               3,301,607             (4,727,876)
Cash and cash equivalents at beginning of period                  26,027,235             30,818,689
                                                                ------------           ------------
Cash and cash equivalents at end of period                      $ 29,328,842           $ 26,090,813
                                                                ============           ============
</TABLE>



    The accompanying notes are an integral part of the financial statements.



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                                 ENTREMED, INC.
                   NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
                           MARCH 31, 2000 (UNAUDITED)



1.          BASIS OF PRESENTATION

            Our accompanying unaudited consolidated financial information
            includes the accounts of our 85% owned subsidiary, Cytokine
            Sciences, Inc. Cytokine Sciences was formed in June 1996 and was
            capitalized with $250,000 from us for the purpose of acquiring the
            assets of Innovative Therapeutics, Inc., which acquisition was
            completed in July 1996 in exchange for 15% of the common stock of
            Cytokine Sciences, Inc.

            The accompanying unaudited consolidated financial statements have
            been prepared in accordance with generally accepted accounting
            principles for interim financial information and in accordance with
            the instructions to Form 10-Q and Article 10 of Regulation S-X.
            Accordingly, such consolidated financial statements do not include
            all of the information and disclosures required by generally
            accepted accounting principles for complete financial statements. In
            the opinion of our management, all adjustments (consisting of normal
            recurring accruals) considered necessary for a fair presentation
            have been included. Operating results for the three month period
            ended March 31, 2000 are not necessarily indicative of the results
            that may be expected for the year ending December 31, 2000. For
            further information, refer to our audited financial statements and
            footnotes thereto included in our Form 10-K for the year ended
            December 31, 1999.

2.          CONTINGENCIES

            We are a defendant in a lawsuit initiated in August 1995 in the
            United States District Court for the Eastern District of Tennessee
            by Bolling, McCool & Twist ("BMT"), a consulting firm. In the suit,
            BMT asserts that we breached an agreement between BMT and us by
            failing to pay BMT certain fees it asserts are owed under the
            agreement. More specifically, BMT has asserted a claim for the
            payment of services rendered in the approximate amount of $50,000
            and seeks a success fee in an unspecified amount in connection with
            the BMS Collaboration. The judge in the case bifurcated the
            proceeding into two phases: an adjudication of whether we breached
            our agreement with BMT and then a damage phase. After a trial on the
            merits the jury found in favor of BMT on the breach of contract
            claim. A trial to determine damages had been scheduled for April 14,
            1998. However, on April 6, 1998, the court issued an Order pursuant
            to which damages were limited to those arising during the term of
            the Agreement, which terminated on November 1, 1995. On May 6, 1999,
            the court confirmed its decision by granting our motion for summary
            judgement and limiting our damages to approximately $50,000 plus
            interest. Thus, this litigation at the trial level has been
            concluded. BMT has filed an appeal and we have cross-appealed. We
            can not predict the outcome of such appeal. However, we intend to
            continue to contest any further action vigorously and believe that
            this proceeding will not have a material adverse effect on us or on
            our financial condition, although there can be no assurance that
            this will be the case.






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ITEM 2. MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS
OF OPERATIONS.

OVERVIEW

            Since our inception in September 1991, we have devoted substantially
all of our efforts and resources to sponsoring and conducting research and
development on our own behalf and through collaborations. Through March 31,
2000, with the exception of license fees, research and development funding,
royalty payments, and certain research grants, we have not generated any revenue
from operations. We anticipate our primary revenue sources for the next several
years to include royalty payments, research grants and collaboration payments
from collaborators under arrangements entered into in the future. The timing and
amounts of such revenues, if any, will likely fluctuate and depend upon the
achievement of specified research and development milestones, and results of
operations for any period may be unrelated to the results of operations for any
other period.

RESULTS OF OPERATIONS

Three Months Ended March 31, 2000 and March 31, 1999

            Revenues decreased approximately 50% from approximately $1,444,000
for the three months ended March 31, 1999 ("1999 Three Months") to approximately
$727,000 for the three months ended March 31, 2000 ("2000 Three Months"). This
decrease results from the absence of BMS collaborative research and development
fees and license fees due to the modification of the research agreement whereby
the we assumed all responsibility for preclinical and clinical work on the
Angiostatin protein. BMS collaborative research and development fees and license
fees recognized totaled approximately $1,092,000 for the 1999 Three Months.
Royalty income increased approximately 173% from approximately $192,000 for the
1999 Three Months to approximately $525,000 for the 2000 Three Months. This
increase is primarily due to royalty income received from Celgene on the sale of
THALOMID(R).

            Research and development expenses increased by approximately 28%
from approximately $7,107,000 for the 1999 Three Months to approximately
$9,071,000 for the 2000 Three Months. Research and development expenditures
include sponsored research payments to academic collaborators, including
payments to Children's Hospital of $700,000 in 2000 and $1,000,000 in 1999 and
expenses related to our internal research programs. The increase in internal
research expenses resulted primarily from the increased efforts in manufacturing
of our three product candidates, Endostatin, Angiostatin and 2ME2, to support
our clinical trial programs, and our internal and sponsored research and product
development programs related to our antiangiogenesis and blood cell permeation
technologies. Overall, research personnel increased from 45 as of March 31, 1999
to 67 as of March 31, 2000. Research and development expenses are expected to
continue to increase as we continue to expand our research and development
efforts.

            General and administrative expenses increased approximately 42% from
approximately $1,896,000 for the 1999 Three Months to approximately $2,697,000
for the 2000 Three Months. The 2000 Three Months increase resulted primarily
from the increase in administrative costs associated with adding administrative
staff to support our research efforts and external collaborations we are
conducting, investigating potential strategic relationships, and obtaining
professional services. Investment income increased approximately 10% from
approximately $410,000 for the 1999 Three Months to approximately $450,000 for
the 2000 Three Months.



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LIQUIDITY AND CAPITAL RESOURCES

            We anticipate incurring substantial additional losses over at least
the next several years due to, among other factors, the need to expend
substantial amounts on our ongoing and planned clinical trials, additional
research and development activities, and related business development and
general corporate expenses. From inception through March 31, 2000, we have
financed our operations from:

      -     the net proceeds of private placements of equity securities which
            raised approximately $17,000,000;
      -     payments from Bristol-Myers Squibb, including $9,700,000 received in
            December 1995 (of which $6,500,000 was an equity investment),
            $11,535,000 received in 1996 (of which $5,000,000 was an equity
            investment), $3,670,000 in each of the years 1997 and 1998, $611,667
            in 1999;
      -     various grants from the World Health Organization and SBIR grants
            totaling approximately $1,371,000;
      -     our June 1996 Initial Public Offering ("IPO") which raised net
            proceeds of approximately $43,541,000;
      -     proceeds of approximately $654,000 under capital leases;
      -     a private offering completed on July 27, 1999 of 1,478,118 shares of
            our common stock, Series 1 Warrants to purchase a total of 739,059
            shares of common stock at an exercise price of $33.02 and Series 2
            Warrants to purchase a total of 739,059 shares of common stock at an
            exercise price of $25.45, resulting in net proceeds to us of
            approximately $28,400,000;
      -     redeemable warrants issued in connection with the private offering
            which have resulted in additional proceeds to us of approximately
            $12,700,000 through March 31, 2000; and
      -     proceeds of $3,000,000 from a borrowing in December 1999 secured by
            substantially all of our furniture and equipment.

            In connection with the private offering completed on July 27, 1999
described above, the Series 2 Warrants are terminable by us at any time after
April 22, 2000 if our common stock trades at a per share price greater than
$38.18 for ten consecutive trading days and such Warrants are not exercised
within a specified period after our delivery of a written notice. The Series 1
Warrants are terminable by us at any time after January 27, 2002 if our common
stock trades at a per share price greater than $61.91 for ten consecutive
trading days and such Warrants are not exercised within a specified period after
our delivery of a written notice. If the Series 2 Warrants were fully exercised,
they would result in us receiving $18,800,000 in aggregate exercise proceeds. If
the Series 1 Warrants were fully exercised, they would result in us receiving
$24,400,000 in aggregate exercise proceeds.

            In December 1999, we exercised our option to repurchase 291,667 of
our common shares from BMS for $13.143 a share or a total repurchase price of
$3,833,379 and which is reflected as treasury stock in the accompanying
consolidated balance sheets. BMS's remaining 583,332 shares held in connection
with the collaborative research and development agreement are subject to certain
restrictions, including future repurchase rights which expire in December 2000
and 2001.

            At March 31, 2000, we had cash and cash equivalents of approximately
$29,329,000 with working capital of approximately $24,952,000, primarily
representing the net proceeds of our private placements of equity securities and
our initial public offering, payments from BMS which include equity investments,
royalties received from Celgene, proceeds from secured borrowing and various
grants.





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<PAGE>   9

            Our cash resources have been used to finance research and
development, including sponsored research, capital expenditures, including
leasehold improvements to our new facility, and general and administrative
expenses. Over the next several years, we expect to incur substantial additional
research and development costs, including costs related to early-stage research,
preclinical and clinical trials, product manufacturing, increased administrative
expenses to support our research and development operations and increased
capital expenditures for expanded research capacity, various equipment needs and
facility improvements.

            We are a party to sponsored research agreements requiring us to fund
an aggregate of approximately $2,153,000 through 2001 (including $1,550,000 to
Children's Hospital, Boston); a materials production agreement of an estimated
$9,000,000 for clinical trials; license agreements requiring future milestone
payments of up to $3,435,000; and additional payments upon attainment of
regulatory milestones.

            We believe that our existing resources will be sufficient to meet
our planned expenditures over the next twelve months, although there can be no
assurance we will not require additional funds. Our working capital requirements
will depend upon numerous factors including:

      -     the progress of our research and development programs;
      -     preclinical testing and clinical trials;
      -     achievement of regulatory milestones;
      -     our potential corporate partners fulfilling their obligations to us;
      -     the timing and cost of seeking regulatory approvals;
      -     the level of resources that we devote to the development of
            manufacturing, marketing and sales capabilities, if any;
      -     technological advances;
      -     the status of competing products; and
      -     our ability to maintain existing and establish new collaborative
            arrangements with other companies to provide us with funding to
            support these activities.

            We will require substantial funds in addition to the present
existing working capital to develop our product candidates and to meet our
business objectives.





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<PAGE>   10





PART II.       OTHER INFORMATION

Item 1.        LEGAL PROCEEDINGS

               This information as set forth in Note 2 of "Notes to Consolidated
Financial Statements" appearing in Item 1 of Part I of this report is
incorporated herein by reference.

Item 2.        CHANGES IN SECURITIES

               Not applicable.

Item 3.        DEFAULT UPON SENIOR SECURITIES

               Not applicable.

Item 4.        SUBMISSION OF MATTERS TO VOTE OF SECURITY HOLDERS

               Not applicable

Item 5.        OTHER INFORMATION

               Not applicable.

Item 6.        EXHIBITS AND REPORTS ON FORM 8-K

               Not applicable


               27.1           Financial Data Schedule






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                                   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.



                                                  ENTREMED, INC.
                                                   (Registrant)


Date:  May 12, 2000                            /s/ John W. Holaday
                                       --------------------------------------
                                             John W. Holaday, Ph.D.
                                      President and Chief Executive Officer




Date:  May 12, 2000                            /s/ R. Nelson Campbell
                                       --------------------------------------
                                                R. Nelson Campbell
                                               Chief Financial Officer





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