<PAGE>   1
================================================================================

                       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 [NO FEE REQUIRED]

                  For the Quarterly Period Ended March 31, 2000

                                       OR

    (  ) TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES
         EXCHANGE ACT OF 1934 [NO FEE REQUIRED]

    For the transition period from _________ to _________

                           Commission File No. 0-20111

                          ARONEX PHARMACEUTICALS, INC.
             (Exact name of Registrant as specified in its charter)

              Delaware                                         76-0196535
   (State or other jurisdiction                            (I.R.S. Employer
  of incorporation or organization)                        Identification No.)

          8707 Technology Forest Place, The Woodlands, Texas 77381-1191
               (Address of principal executive office) (Zip Code)

       Registrant's telephone number, including area code: (281) 367-1666

         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 latest practicable date.

               CLASS                              OUTSTANDING AT MARCH 31, 2000
    -----------------------------                 -----------------------------
    Common Stock, $.001 par value                        22,922,078 shares


================================================================================


<PAGE>   2
                  ARONEX PHARMACEUTICALS, INC. AND SUBSIDIARIES
                      QUARTERLY PERIOD ENDED MARCH 31, 2000

                                      INDEX

<TABLE>
<CAPTION>

                                                                                                               PAGE
                                                                                                               ----

<S>                                                                                                           <C>
Factors Affecting Forward-Looking Statements................................................................      3

PART I.           FINANCIAL INFORMATION

Item 1   Consolidated Financial Statements..................................................................      3

         Consolidated Balance Sheets - December 31, 1999 and March 31, 2000 (unaudited).....................      4

         Consolidated Statements of Operations:
           Three Months Ended March 31, 1999 and March 31, 2000
           (unaudited) and for the Period from Inception (June 13, 1986)
           through March 31, 2000 (unaudited)...............................................................      5

         Consolidated Statements of Comprehensive Income:
           Three Months Ended March 31, 1999 and March 31, 2000 (unaudited).................................      5

         Consolidated Statements of Cash Flows:
           Three Months Ended March 31, 1999 and March 31, 2000
           (unaudited) and for the Period from Inception (June 13, 1986)
           through March 31, 2000 (unaudited)...............................................................      6

         Notes to Consolidated Financial Statements - March 31, 2000 (unaudited)............................      7

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

Item 3   Qualitative and Quantitative Disclosures about Market Risk.........................................     11


PART II.           OTHER INFORMATION

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


SIGNATURES        ..........................................................................................     12
</TABLE>




                                      -2-
<PAGE>   3


FACTORS AFFECTING FORWARD-LOOKING STATEMENTS

     This Quarterly Report on Form 10-Q includes "forward-looking statements"
within the meaning of Section 27A of the Securities Act of 1933, as amended, and
Section 21E of the Securities Exchange Act of 1934, as amended (the "Exchange
Act"). When used in this document, the words "anticipate," "believe," "expect,"
"estimate," "project" and similar expressions are intended to identify
forward-looking statements. Such statements are subject to certain risks,
uncertainties and assumptions. Should one or more of these risks or
uncertainties materialize, or should underlying assumptions prove incorrect,
actual results may vary materially from those anticipated, believed, expected,
estimated or projected. For additional discussion of such risks, uncertainties
and assumptions, see "Item 1. Business -- Manufacturing," "-- Sales and
Marketing," "-- Patents and Proprietary Rights," "-- Government Regulation," "--
Competition" and "-- Additional Business Risks" included in the Company's Annual
Report on Form 10-K/A for the year ended December 31, 1999.

PART I.  FINANCIAL INFORMATION

ITEM 1.  CONSOLIDATED FINANCIAL STATEMENTS

     The following unaudited consolidated financial statements have been
prepared pursuant to the rules and regulations of the Securities and Exchange
Commission. Certain information and note disclosures normally included in annual
financial statements prepared in accordance with generally accepted accounting
principles have been condensed or omitted pursuant to those rules and
regulations, although we believe that the disclosures made herein are adequate
to make the information presented not misleading. These consolidated financial
statements should be read in conjunction with the audited financial statements
for the year ended December 31, 1999 included in our Annual Report on Form
10-K/A for the year ended December 31, 1999, filed pursuant to Section 13 or
15(d) of the Exchange Act.

     The information presented in the accompanying consolidated financial
statements is unaudited, but in the opinion of management, reflects all
adjustments (which include only normal recurring adjustments) necessary to
present fairly such information.




                                      -3-
<PAGE>   4

                  ARONEX PHARMACEUTICALS, INC. AND SUBSIDIARIES
                          (A DEVELOPMENT STAGE COMPANY)

                           CONSOLIDATED BALANCE SHEETS
                  (ALL AMOUNTS IN THOUSANDS, EXCEPT SHARE DATA)
<TABLE>
<CAPTION>


                                                         ASSETS
                                                                                                     MARCH 31,
                                                                                   DECEMBER 31,       2000
                                                                                       1999        (UNAUDITED)
                                                                                   ------------    ------------
<S>                                                                                <C>             <C>
Current assets:
   Cash and cash equivalents ...................................................   $     11,528    $     13,158
   Short-term investments ......................................................          7,804              --
   Prepaid expenses and other assets ...........................................            453             404
                                                                                   ------------    ------------
        Total current assets ...................................................         19,785          13,562

Long-term investments ..........................................................            920             916
Furniture, equipment and leasehold improvements, net of accumulated
   depreciation of $3,450 and $3,599, respectively .............................          2,029           1,948
                                                                                   ------------    ------------
        Total assets ...........................................................   $     22,734    $     16,426
                                                                                   ============    ============

                                            LIABILITIES AND STOCKHOLDERS' EQUITY
Current liabilities:
   Accounts payable and accrued expenses .......................................   $      3,502    $      2,750
   Accrued payroll .............................................................            644             454
   Current portion of notes payable ............................................            340             350
                                                                                   ------------    ------------
        Total current liabilities ..............................................          4,486           3,554

Long-term liabilities:
   Notes payable, net of current portion .......................................          3,517           3,447
                                                                                   ------------    ------------
        Total long-term liabilities ............................................          3,517           3,447

Commitments and contingencies

Stockholders' equity:
   Preferred stock $.001 par value, 5,000,000 shares authorized,
        none issued and outstanding ............................................             --              --
   Common stock $.001 par value, 40,000,000 shares authorized,
        22,853,782 and 22,922,078 shares issued and outstanding,
        respectively ...........................................................             23              23
   Additional paid-in capital ..................................................        113,262         113,538
   Common Stock warrants .......................................................            908             908
   Treasury stock ..............................................................            (11)            (11)
   Deferred compensation .......................................................            (69)            (52)
   Unrealized gain on investments ..............................................          2,147              --
   Deficit accumulated during development stage ................................       (101,529)        104,981)
                                                                                   ------------    ------------
        Total stockholders' equity .............................................         14,731           9,425
                                                                                   ------------    ------------
   Total liabilities and stockholders' equity ..................................   $     22,734    $     16,426
                                                                                   ============    ============
</TABLE>



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

                                      -4-
<PAGE>   5

                  ARONEX PHARMACEUTICALS, INC. AND SUBSIDIARIES
                          (A DEVELOPMENT STAGE COMPANY)

                      CONSOLIDATED STATEMENTS OF OPERATIONS
             (ALL AMOUNTS IN THOUSANDS, EXCEPT LOSS PER SHARE DATA)
                                   (UNAUDITED)

<TABLE>
<CAPTION>

                                                                                         PERIOD FROM
                                                                                          INCEPTION
                                                                                          (JUNE 13,
                                                              THREE MONTHS ENDED            1986)
                                                                  MARCH 31,                THROUGH
                                                         ----------------------------     MARCH 31,
                                                            1999            2000            2000
                                                         ------------    ------------    ------------
<S>                                                      <C>             <C>             <C>
Revenues:
   Interest income ...................................   $        304    $        221    $      8,397
   Research and development grants and contracts .....          3,282             300          23,139
                                                         ------------    ------------    ------------
        Total revenues ...............................          3,586             521          31,536
                                                         ------------    ------------    ------------
Expenses:
   Research and development ..........................          5,934           5,800         103,222
   Purchase of in-process research and development ...             --              --          11,625
   General and administrative ........................            785             699          22,509
   Interest expense and other ........................             42             127           1,814
                                                         ------------    ------------    ------------
        Total expenses ...............................          6,761           6,626         139,170
                                                         ------------    ------------    ------------

Operating loss .......................................   $     (3,175)   $     (6,105)   $   (107,634)
                                                         ------------    ------------    ------------

Other income:
   Gain on sale of investments .......................             --           2,653           2,653
                                                         ------------    ------------    ------------

Net loss .............................................   $     (3,175)   $     (3,452)   $   (104,981)
                                                         ============    ============    ============

Basic and diluted loss per share .....................   $      (0.17)   $      (0.15)
                                                         ============    ============

Weighted average shares used in computing basic and
   diluted loss per share ............................         18,894          22,881

</TABLE>



                  ARONEX PHARMACEUTICALS, INC. AND SUBSIDIARIES
                          (A DEVELOPMENT STAGE COMPANY)

                 CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME
             (ALL AMOUNTS IN THOUSANDS, EXCEPT LOSS PER SHARE DATA)
                                  (UNAUDITED)

<TABLE>
<CAPTION>

                                                            THREE MONTHS ENDED
                                                                 MARCH 31,
                                                         -------------------------
                                                            1999           2000
                                                         -----------   -----------
<S>                                                      <C>           <C>
Comprehensive income:
    Net loss .........................................   $    (3,175)  $    (3,452)
    Unrealized gain on securities available for sale..           101            --
                                                         -----------   -----------
        Comprehensive income .........................   $    (3,074)  $    (3,452)
                                                         ===========   ===========
</TABLE>

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

                                      -5-


<PAGE>   6

                  ARONEX PHARMACEUTICALS, INC. AND SUBSIDIARIES
                          (A DEVELOPMENT STAGE COMPANY)

                      CONSOLIDATED STATEMENTS OF CASH FLOWS
                           (ALL AMOUNTS IN THOUSANDS)
                                   (UNAUDITED)
<TABLE>
<CAPTION>
                                                                                                           PERIOD FROM
                                                                                                            INCEPTION
                                                                                                         (JUNE 13, 1986)
                                                                                 THREE MONTHS ENDED          THROUGH
                                                                                       MARCH 31,             MARCH 31,
                                                                              --------------------------
                                                                                1999            2000           2000
                                                                              -----------    -----------    -----------
<S>                                                                           <C>            <C>            <C>
Cash flows from operating activities:
   Net loss ...............................................................   $    (3,175)   $    (3,452)   $  (104,981)
   Adjustments to reconcile net loss to net cash provided by
     (used in) operating activities-
        Depreciation and amortization .....................................           167            149          5,607
        Loss (gain) on disposal of assets .................................            (1)            --            200
        Gain on sale of investments .......................................            --         (2,653)        (2,653)
        Compensation expense related to stock and stock options ...........           280            171          5,038
        Charge for purchase of in-process research and development ........            --             --         11,547
        Unrealized gain on investment .....................................           101         (2,147)            --
        Acquisition costs, net of cash received ...........................            --             --           (270)
        Accrued interest payable converted to stock .......................            --             --             97
        Loss in affiliate .................................................            --             --            500
   Changes in assets and liabilities:
        Increase in prepaid expenses and other assets .....................          (219)            49           (219)
        Decrease (increase) in accounts receivable ........................          (196)            --             --
        Increase (decrease) in accounts payable and accrued expenses ......          (587)          (942)         3,131
        Decrease in deferred revenue ......................................            --             --           (353)
                                                                              -----------    -----------    -----------
                  Net cash used in operating activities ...................        (3,630)        (8,825)       (82,356)

Cash flows from investing activities:
   Purchases of investments ...............................................       (13,815)            --       (261,361)
   Sales of investments ...................................................         5,015         10,461        268,833
   Purchase of furniture, equipment and leasehold improvements ............           (77)           (68)        (6,524)
   Proceeds from sale of assets ...........................................            --             --             63
   Investment in affiliate ................................................            --             --           (500)
                                                                              -----------    -----------    -----------
                  Net cash provided by (used in) investing activities .....        (8,877)        10,393            511

Cash flows from financing activities:
   Proceeds from notes payable ............................................           547             12          6,980
   Repayment of notes payable and principal payments under capital
     lease obligations ....................................................           (70)           (72)        (3,184)
   Purchase of treasury stock .............................................            --             --            (11)
   Proceeds from issuance of stock ........................................        11,699            122         91,218
                                                                              -----------    -----------    -----------
                  Net cash provided by (used in) financing activities .....        12,176             62         95,003
                                                                              -----------    -----------    -----------

Net increase (decrease) in cash and cash equivalents ......................          (331)         1,630         13,158
Cash and cash equivalents at beginning of period ..........................        11,338         11,528             --
                                                                              -----------    -----------    -----------

Cash and cash equivalents at end of period ................................   $    11,007    $    13,158    $    13,158
                                                                              ===========    ===========    ===========
Supplemental disclosures of cash flow information:
   Cash paid during the period for interest ...............................   $        43    $       177    $     1,316
Supplemental schedule of noncash financing activities:
   Conversion of notes payable and accrued interest to common stock .......   $        --    $        --    $     3,043
</TABLE>





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



                                      -6-
<PAGE>   7

                  ARONEX PHARMACEUTICALS, INC. AND SUBSIDIARIES
                          (A DEVELOPMENT STAGE COMPANY)

                   NOTES TO CONSOLIDATED FINANCIAL STATEMENTS

                                 MARCH 31, 2000
                                   (UNAUDITED)

1.   ORGANIZATION

     Aronex Pharmaceuticals, Inc. ("the Company", "Aronex Pharmaceuticals",
"we", "us" or "our") was incorporated in Delaware on June 13, 1986 and merged
with Triplex Pharmaceutical Corporation ("Triplex") and API Acquisition Company,
Inc. ("API"), formerly Oncologix, Inc. effective September 11, 1995. In 1998, we
formed a subsidiary, Aronex Europe Limited.

     Aronex Pharmaceuticals is a development stage company that has devoted
substantially all of its efforts to research and product development and has not
yet generated any significant revenues, nor is there any assurance of future
revenues. In addition, we expect to continue to incur losses for the foreseeable
future, and there can be no assurance that we will successfully complete the
transition from a development-stage company to successful operations. The
research and development activities we engage in involve a high degree of risk
and uncertainty. Our ability to successfully develop, manufacture and market our
proprietary products is dependent upon many factors. These factors include, but
are not limited to, the need for additional financing attracting and retaining
key personnel and consultants, and successfully developing manufacturing, sales
and marketing operations. Our ability to develop these operations may be
immensely impacted by uncertainties related to patents and proprietary
technologies, technological change and obsolescence, product development,
competition, government regulations and approvals, health care reform,
third-party reimbursement and product liability exposure. Additionally, we are
reliant upon collaborative arrangements for research, contractual agreements
with corporate partners, and our exclusive license agreements with The
University of Texas M.D. Anderson Cancer Center. Further, during the period
required to develop these products, we will require additional funds which may
not be available to us. We believe that we can conserve our current cash
resources to satisfy our funding needs into mid 2001. Accordingly, there can be
no assurance of our future success. See "Business -- Additional Business Risks"
in our Form 10-K/A for the year ended December 31, 1999.

     The consolidated balance sheet at March 31, 2000 and the related
consolidated statements of operations and cash flows for the three month periods
ending March 31, 2000 and 1999 and the period from inception (June 13, 1986)
through March 31, 2000 are unaudited. These interim financial statements should
be read in conjunction with the audited financial statements and related notes
included in our 1999 Form 10- K/A. The unaudited interim consolidated financial
statements reflect all adjustments which are, in the opinion of management,
necessary for a fair statement of results for the interim periods presented and
all such adjustments are of a normal recurring nature. Interim results are not
necessarily indicative of results for a full year.

2.   ACCOUNTING POLICIES

     Principles of Consolidation

     The consolidated financial statements include the accounts of Aronex
Pharmaceuticals, Triplex, API and Aronex Europe Limited. All material
intercompany transactions have been eliminated in consolidation.

     Cash, Cash Equivalents and Short- and Long-Term Investments

     Cash and cash equivalents include money market accounts and investments
with an original maturity of less than three months. Long-term investments at
March 31, 2000 are available for sale securities which are United States
mortgage-backed securities with maturity dates over the next 23 years that have
an amortized cost of $916,000, which approximates fair market value and cost.
Aronex Pharmaceuticals currently has no trading securities.

                                      -7-
<PAGE>   8

                  ARONEX PHARMACEUTICALS, INC. AND SUBSIDIARIES
                          (A DEVELOPMENT STAGE COMPANY)

     New Accounting Pronouncements

     In December 1999, the Securities and Exchange commission (SEC) issued Staff
Accounting Bulletin 101, "Revenue Recognition in Financial Statements" (SAB 101)
which provides guidance related to revenue recognition based on interpretations
and practices followed by the SEC. SAB 101 is effective the second fiscal
quarter of fiscal years beginning after December 15, 1999 and requires companies
to report any changes in revenue recognition as a cumulative change in
accounting principle at the time of implementation in accordance with Accounting
Principles Board Opinion No. 20, "Accounting Changes." We are currently in the
process of evaluating what impact, if any, SAB 101 will have on our financial
position or our results of operations.

3.   FEDERAL INCOME TAXES

     At December 31, 1999, we had net operating loss ("NOL") carryforwards for
federal income tax purposes of approximately $114.8 million. The Tax Reform Act
of 1986 provided a limitation on the use of NOL and tax credit carryforwards
following certain ownership changes that could limit our ability to utilize
these NOLs and tax credits. Accordingly, our ability to utilize the above NOL
and tax credit carryforwards to reduce future taxable income and tax liabilities
may be limited. As a result of the merger with Triplex and API, a change in
control as defined by federal income tax law occurred, causing the use of these
carryforwards to be limited and possibly eliminated. Additionally, because
United States tax laws limit the time during which NOLs an the tax credit
carryforwards may be applied against future taxable income and tax liabilities,
we may not be able to take full advantage of our NOLs and tax credit
carryforwards for federal income tax purposes. The carryforwards will begin to
expire in 2001 if not otherwise used. Due to the possibility of not reaching a
level of profitability that will allow for the utilization of our deferred tax
assets, a valuation allowance has been established to offset these tax assets.
We have not made any federal income tax payments since inception.

4.   SUBSEQUENT EVENT

     In April 2000, we raised proceeds net of offering costs of approximately
$7.3 million in a private placement of Units. Each $100,000 Unit is comprised of
(1) shares of our common stock in an amount determined by dividing $100,000 by
$2.75 and (2) a warrant with a five-year term to purchase an amount of shares of
our common stock that is one third of the amount of shares contained in such
Unit at an exercise price of $3.00 per share. Through these units, we issued
2,932,574 shares of common stock and warrants to purchase 977,524 shares of
common stock. In addition, we paid a finder, who assisted us in placing the
common stock, a placement fee of 7% of the gross proceeds and issued warrants
with a seven-year term to purchase 150,000 shares of our common stock at an
exercise price of $3.25 per share. The fair value of the warrants issued,
$2,560,780, will be recorded in our second quarter 2000 financial statements.
This amount has been estimated on the date of the grant using the Black Scholes
option pricing model with the following weighted-average assumptions: a risk
free rate of 5.6%, with no expected dividends, expected lives of 5 and 7 years
and expected volatility of 92%.


                                      -8-

<PAGE>   9

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

RESULTS OF OPERATIONS

     OVERVIEW

     Since our inception in 1986, we have primarily devoted our resources to
fund research, drug discovery and development. We have been unprofitable to date
and expect to incur substantial operating losses for the next several years as
we expend our resources for product research and development, preclinical and
clinical testing and regulatory compliance. We have sustained losses of $105
million through March 31, 2000. Our research and development activities and
operations have been financed primarily through public and private offerings of
securities and, to a lesser extent, from revenues under research and development
grants and contracts. Our operating results have fluctuated significantly during
each quarter, and we anticipate that these fluctuations, largely attributable to
varying commitments and expenditures for clinical trials and research and
development, will continue for the next several years.

     Three Month Periods Ended March 31, 1999 and 2000

     Revenues from research and development grants and contracts decreased 90.9%
to $300,000 in 2000 from $3.3 million in 1999. This decrease was due to a
decrease of $3.0 million in milestone and development payments received relating
to our license agreement for Nyotran(R) with Abbott Laboratories ("Abbott") in
the first quarter of 2000.

     Interest income decreased 27% to $221,000 in 2000 from $304,000 in 1999.
The decrease in interest income resulted from a decrease in the average amount
of funds available for investment during the first three months of 2000.

     Research and development expenses decreased 2% to $5.8 million in 2000 from
$5. million in 1999. This decrease resulted from the following:

     o    a decrease of $1.2 million in clinical trial costs relating to
          Nyotran(R); and
     o    a decrease of $633,000 in salaries and payroll costs.

These decreases were partially offset by:

     o    an increase of $1.0 million in clinical trial costs relating to
          ATRAGEN(R);
     o    an increase of $187,000 in regulatory consultants; and
     o    an increase of $478,000 in drug materials and manufacturing relating
          mostly to ATRAGEN(R) and Annamycin.

     General and administrative expenses decreased 11% to $699,000 in 2000 from
$785,000 in 1999. The decrease in general and administrative expenses resulted
primarily from a decrease in marketing expenses in the first quarter of 2000.

     Interest expense was $127,000 and $42,000 for the three months ended March
31, 2000 and 1999, respectively. The $85,000 increase in interest expense
resulted primarily from the following:

     o    an increase in the balance of notes payable obtained to finance
          furniture and equipment; and
     o    an increase of $2.5 million in notes payable relating to a promissory
          not issued to Genzyme in the second quarter of 1999.

     Other income of $2,653,000 in the first quarter of 2000 represents a gain
on the sale of Targeted Genetics common stock, which had a carrying value of
zero.

                                      -9-
<PAGE>   10

LIQUIDITY AND CAPITAL RESOURCES

     Since our inception, our primary source of cash has been from financing
activities, which have consisted primarily of sales of equity securities, and to
a lesser extent, from revenues under research and development agreements and
grants. We have raised an aggregate of $91.2 million from the sale of equity
securities from inception through March 31, 2000. In addition, we have received
$22.6 million since inception relating to research and development grants and
contracts. In April 2000, we raised net proceeds of approximately $7.3 million
in a private placement of 2,932,574 shares of our common stock.

     The majority of our development activities are committed on a short-term,
as-needed basis through contracts and purchase orders. These arrangements can
be changed based on our needs and development activities. We have contracted
with certain clinical research and other consulting organizations to assist in
conducting our clinical trials. The agreements provide that we can terminate
them at any time, should either our financial situation, or the results of the
studies, require it. Nonetheless, we intend to continue to engage such services
in the future.

     Our primary use of cash to date has been in operating activities to fund
research and development, including preclinical studies and clinical trials and
general and administrative expenses. Cash of $8.8 million and $3.6 million was
used in operating activities during the first quarter of 2000 and 1999,
respectively. We had cash, cash-equivalents and long-term investments of $14.1
million as of March 31, 2000, consisting primarily of cash and money market
accounts, and United States government securities and investment grade
commercial paper.

     We have experienced negative cash flows from operations since inception. We
have expended, and will continue to require, substantial funds to continue our
research and development activities, including preclinical studies and clinical
trials of our products, and to commence sales and marketing efforts if the U.S.
Food and Drug Administration and other regulatory approvals are obtained. We
believe that we can conserve our existing financial resources to satisfy our
capital and operating requirements into mid-2001. In the future, we expect that
we will need to raise substantial additional capital to fund our operations.

     We have experienced significant fluctuations in accounts payable and
accrued payroll primarily as a result of the development activities relating to
our products. We anticipate that the amounts expended for these items in the
future will continue to correspond with our development activities. If the
volume of development activities decreases, there will be a decrease in
outstanding payables and a decrease in our liquidity position. We expect that
our expenses relating to development activities will fluctuate from quarter to
quarter over the next few years as we have not yet generated revenues from
product sales. Also, we have typically obtained debt financing when necessary
for equipment, furniture and leasehold improvement requirements. We expect that
we will continue to incur additional debt to meet our capital requirements from
time to time in the future based on our financial resources and needs.

     Our capital requirements will depend on many factors, including the risk
factor more completely described under "Business -- Additional Business Risks"
in our 1999 Form 10-K/A. These factors include:

     o    problems, delays, expenses and complications frequently encountered by
          development stage companies;
     o    the progress of our research, development and clinical trial programs;
     o    the extent and terms of any future collaborative research,
          manufacturing, marketing or other funding arrangements;
     o    the costs and timing of seeking regulatory approvals of our products;
     o    our ability to obtain regulatory approvals;
     o    the success of our sales and marketing programs;
     o    the costs of filing, prosecuting, defending and enforcing any patent
          claims and other intellectual property rights; and
     o    changes in economic, regulatory or competitive conditions of our
          planned business.


                                      -10-
<PAGE>   11



     Estimates about the adequacy of funding for our activities are based on
certain assumptions, including the assumption that testing and regulatory
procedures relating to our products can be conducted at projected costs. There
can be no assurance that changes in our research and development plans,
acquisitions or other events will not result in accelerated or unexpected
expenditures.

     To satisfy our capital requirements, we may seek to raise additional funds
in the public or private capital markets. Our ability to raise additional funds
in the public or private markets will be adversely affected if the results of
our current or future clinical trials are not favorable. We may seek additional
funding through corporate collaborations and other financing vehicles. There can
be no assurance that any funding will be available to us on favorable terms or
at all. If adequate funds are not available, we may be required to curtail
significantly one or more of our research or development programs, or we may be
required to obtain funds through arrangements with future collaborative partners
or other parties that may require us to relinquish rights to some or all of our
technologies or products. If we are successful in obtaining additional financing
for the Company, the terms of such financing may have the effect of diluting or
adversely affecting the holdings or the rights of the holders of our common
stock.

     In December 1999, the Securities and Exchange commission (SEC) issued Staff
Accounting Bulletin 101, "Revenue Recognition in Financial Statements" (SAB 101)
which provides guidance related to revenue recognition based on interpretations
and practices followed by the SEC. SAB 101 is effective the second fiscal
quarter of fiscal years beginning after December 15, 1999 and requires companies
to report any changes in revenue recognition as a cumulative change in
accounting principle at the time of implementation in accordance with Accounting
Principles Board Opinion No. 20, "Accounting Changes." We are currently in the
process of evaluating what impact, if any, SAB 101 will have on our financial
position or our results of operations


ITEM 3. QUALITATIVE AND QUANTITATIVE DISCLOSURES ABOUT MARKET RISK

     Not Applicable




PART II. OTHER INFORMATION

ITEM 6. EXHIBITS AND REPORTS ON FORM 8-K

     (a) Exhibits

             11.1 Statement regarding computation of per share earnings.

             27.1 Financial data schedule.

     (b) Reports on Form 8-K

             None


                                      -11-
<PAGE>   12

                                   SIGNATURES

     Pursuant to the requirements of the Securities Exchange Act of 1934, as
amended the Registrant has duly caused this report to be signed on its behalf by
the undersigned, thereunto duly authorized.



                                               ARONEX PHARMACEUTICALS, INC.




Dated:  May 11, 2000                           By:/s/ GEOFFREY F. COX
                                               ---------------------------------
                                               Geoffrey F. Cox, Ph.D.
                                               Chief Executive Officer




Dated:  May 11, 2000                           By: /s/ TERANCE A. MURNANE
                                               ---------------------------------
                                               Terance A. Murnane
                                               Controller
                                               (Principal Financial and
                                               Accounting Officer)


                                      -12-

<PAGE>   13

                                 EXHIBIT INDEX

<TABLE>
<CAPTION>

EXHIBIT
NUMBER            DESCRIPTION
------            -----------
<S>               <C>
  11.1            Statement regarding computation of per share earnings.

  27.1            Financial data schedule.
</TABLE>