<PAGE>   1

                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                                   -----------

                                    FORM 10-Q

                                   -----------


             QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(D) OF THE
                         SECURITIES EXCHANGE ACT OF 1934

                  For the quarterly period ended June 30, 2000

                           Commission File No. 0-31261
                           ---------------------------
                               ATHEROGENICS, INC.
             (Exact name of registrant as specified in its charter)


                   GEORGIA                              58-2108232
                   -------                              ----------
        (State of incorporation)      (I.R.S. Employer Identification Number)


                8995 WESTSIDE PARKWAY, ALPHARETTA, GEORGIA 30004
                ------------------------------------------------
   (Address of registrant's principal executive offices, including zip code)


                                   -----------

      (Registrant's telephone number, including area code): (678) 336-2500
                                                            --------------

    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](1) No [ ]

   As of September, 4, 2000, there were 22,975,915 shares of the registrant's
                           common stock outstanding.

-----------------
 (1)The registrant commenced its initial public offering of common stock on
  August 9, 2000 and closed the offering on August 14, 2000. The registrant has
        filed all reports required to be filed by Section 13 or 15(d) of
                  the Securities Exchange Act of 1934, but it
     has not been subject to such filing requirements for the past 90 days.

<PAGE>   2

                               ATHEROGENICS, INC.

                                    FORM 10-Q

                                      INDEX

<TABLE>

<S>                                                                                                          <C>
PART I. FINANCIAL INFORMATION                                                                                PAGE NO.
                                                                                                             --------

Item 1. Financial Statements.

  Condensed Balance Sheets.                                                                                     3
       June 30, 2000 and December 31, 1999

  Condensed Statements of Operations.
       Three months ended June 30, 2000 and 1999 and six months ended June 30, 2000                             4
       and 1999

  Condensed Statements of Cash Flows.                                                                           5
       Six months ended June 30, 2000 and 1999

  Notes to Condensed Financial Statements.                                                                      6

Item 2. Management's Discussion and Analysis of Financial Condition and Results of Operations.                  8

Item 3. Quantitative and Qualitative Disclosures About Market Risk                                             12

PART II. OTHER INFORMATION

Item 1. Legal Proceedings.                                                                                     13

Item 2. Changes in Securities and Use of Proceeds.                                                             13

Item 3. Defaults Upon Senior Securities.                                                                       13

Item 4. Submission Of Matters To A Vote Of Security Holders                                                    13

Item 5. Other Information.                                                                                     13

Item 6. Exhibits and Reports on Form 8-K.                                                                      14

SIGNATURES                                                                                                     15
</TABLE>


                                       2
<PAGE>   3

                  SECURITIES AND EXCHANGE COMMISSION FORM 10-Q
                         PART I - FINANCIAL INFORMATION

ITEM 1. FINANCIAL STATEMENTS.

                               ATHEROGENICS, INC.
                            CONDENSED BALANCE SHEETS
                                   (UNAUDITED)

<TABLE>
<CAPTION>

                                                                              June 30,             December 31,
                                                                                2000                   1999
                                                                            ------------           ------------
<S>                                                                         <C>                    <C>
ASSETS
Current Assets:
     Cash and cash equivalents ......................................       $  8,677,290           $ 13,409,450
     Receivables ....................................................          1,055,924                791,653
     Interest and other receivables .................................             16,836                 32,708
     Prepaid expenses ...............................................            485,550                 56,911
                                                                            ------------           ------------
              Total current assets ..................................         10,235,600             14,290,722
Equipment and leasehold improvements, net of accumulated
     depreciation ...................................................          1,751,468              1,234,633
Long-term note receivable ...........................................            183,588                191,859
                                                                            ------------           ------------
        Total assets ................................................       $ 12,170,656           $ 15,717,214
                                                                            ============           ============

LIABILITIES, REDEEMABLE CONVERTIBLE PREFERRED
     STOCK AND SHAREHOLDERS' DEFICIT
Current Liabilities:
     Accounts payable ...............................................       $    371,608           $    679,142
     Accrued liabilities ............................................            299,993                285,600
     Accrued development costs ......................................            283,053                240,000
     Current portion of capitalized lease obligation ................            132,349                101,408
     Current portion of deferred revenues ...........................          2,777,778              3,333,333
                                                                            ------------           ------------

              Total current liabilities .............................          3,864,781              4,639,483
Long-term portion of capitalized lease obligation ...................            130,085                 61,854
Long-term portion of deferred revenues ..............................                 --              1,111,111
Redeemable convertible preferred stock:
      Series A, $1 par and liquidation value ........................          1,000,000              1,000,000
      Series B, $3 par and liquidation value ........................         14,164,057             13,704,499
      Series C, $3 par and liquidation value ........................         24,440,231             24,006,992
      Preferred stock warrants ......................................            225,713                481,875
Common shareholders' deficit:
    Common stock no par value:
         Authorized - 21,100,000 shares; issued and outstanding -
         2,961,983 shares at June 30, 2000 and 2,536,543 shares at
         December 1999 ..............................................         14,310,226              2,209,962
Deferred stock compensation .........................................         (9,797,549)            (1,809,680)
Accumulated deficit .................................................        (36,166,888)           (29,688,882)
                                                                            ------------           ------------
       Total common shareholders' deficit ...........................        (31,654,211)           (29,288,600)
                                                                            ------------           ------------
       Total liabilities, redeemable convertible preferred stock
       and shareholders' deficit ....................................       $ 12,170,656           $ 15,717,214
                                                                            ============           ============
</TABLE>

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


                                       3
<PAGE>   4


                               ATHEROGENICS, INC.
                       CONDENSED STATEMENTS OF OPERATIONS
                                   (UNAUDITED)

<TABLE>
<CAPTION>

                                                                   Three Months Ended                      Six Months Ended
                                                                        June 30,                               June 30,
                                                            -------------------------------        -------------------------------
                                                                2000               1999                2000               1999
                                                            ------------       ------------        ------------       ------------
<S>                                                         <C>                <C>                 <C>                <C>
Revenues:
     License fees ...................................       $    833,333       $         --        $  1,666,666       $         --
     Research and development .......................          1,230,717                 --           2,488,664                 --
                                                            ------------       ------------        ------------       ------------
              Total revenues ........................          2,064,050                 --           4,155,330                 --
Operating expenses:
     Research and development, excluding
     amortization of deferred stock
     compensation ...................................          2,728,397          1,616,227           5,614,037          3,817,187

     General and administrative, excluding
     amortization of deferred stock
     compensation ...................................            575,177            754,047           1,361,539          1,181,179

      Amortization of deferred stock compensation ...          1,980,221                225           3,952,059                225
                                                            ------------       ------------        ------------       ------------

              Total operating expenses ..............          5,283,795          2,370,499          10,927,635          4,998,591
                                                            ------------       ------------        ------------       ------------
Operating loss ......................................         (3,219,745)        (2,370,499)         (6,772,305)        (4,998,591)
Net interest income (expense) .......................            136,532           (198,558)            294,299           (320,801)
                                                            ------------       ------------        ------------       ------------
Net loss ............................................       $ (3,083,213)      $ (2,569,057)       $ (6,478,006)      $ (5,319,392)
                                                            ============       ============        ============       ============
Net loss per share - basic and diluted ..............       $      (1.05)      $      (1.06)       $      (2.33)      $      (2.20)
Weighted average shares outstanding -
     basic and diluted ..............................          2,929,823          2,426,521           2,782,819          2,419,323
Pro forma net loss per share - basic and
     diluted ........................................       $       (.18)      $       (.21)       $       (.39)      $       (.52)
Pro forma weighted average shares
     outstanding - basic and diluted ................         16,788,925         12,404,977          16,560,740         10,201,959
</TABLE>

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


                                       4
<PAGE>   5

                               ATHEROGENICS, INC.
                            STATEMENTS OF CASH FLOWS
                                   (UNAUDITED)

<TABLE>
<CAPTION>

                                                                           Six Months            Six Months
                                                                                Ended                 Ended
                                                                        June 30, 2000         June 30, 1999
                                                                        -------------         -------------
<S>                                                                     <C>                   <C>
OPERATING ACTIVITIES
Net Loss .........................................................       $ (6,478,006)          $(5,319,392)
Adjustments to reconcile net loss to net cash used in operating
     activities:
     Depreciation and amortization ...............................            209,369               118,299
     Amortization of deferred stock compensation .................          3,952,059                   225
     Amortization of debt discount ...............................                 --               235,750
     Stock issued for interest ...................................                 --               271,071
     Deferred revenues ...........................................         (1,666,666)                   --
     Changes in operating assets and liabilities:
          Interest and other receivables .........................             24,143            (1,338,165)
          Receivables ............................................           (264,271)                   --
          Prepaid expenses .......................................           (428,639)              (35,296)
          Accounts payable .......................................           (307,534)           (1,175,240)
          Accrued liabilities ....................................             57,446            (1,068,713)
                                                                         ------------           -----------
                  Net cash used in operating activities ..........         (4,902,099)           (8,311,461)
INVESTING ACTIVITIES
Purchases of equipment and leasehold improvements ................           (503,704)             (166,778)

FINANCING ACTIVITIES
Payments on capital lease ........................................           (123,328)              (97,097)
Proceeds from the issuance of preferred stock, Series C ..........                 --             9,608,317
Proceeds from the issuance and exercise of preferred stock
     warrants ....................................................            636,635                    --
Proceeds from the exercise of common stock options ...............            160,336                   844
Proceeds from bridge loan financing, net of warrants .............                 --               150,000
                                                                         ------------           -----------
                  Net cash provided by financing activities ......            673,643             9,662,064
                                                                         ------------           -----------
(Decrease) increase in cash and cash equivalents .................         (4,732,160)            1,183,825
Cash and cash equivalents at beginning of period .................         13,409,450             3,683,423
                                                                         ------------           -----------
Cash and cash equivalents at end of period .......................       $  8,677,290           $ 4,867,248
                                                                         ============           ===========
SUPPLEMENTAL DISCLOSURES OF CASH FLOW INFORMATION
Interest paid ....................................................       $     20,571           $    19,203
Conversion of bridge loan and accrued interest to preferred
     stock .......................................................                 --             6,421,071
Warrants issued for extension of bridge loan .....................                 --               235,750
Equipment purchased under capitalized lease obligation ...........            222,500                    --
</TABLE>

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


                                       5
<PAGE>   6

                               ATHEROGENICS, INC.
                     NOTES TO CONDENSED FINANCIAL STATEMENTS
                                   (UNAUDITED)

1.       BASIS OF PRESENTATION

         The accompanying unaudited interim condensed financial statements
reflect all adjustments (consisting solely of normal recurring adjustments)
which management considers necessary for a fair presentation of the financial
position, results of operations and cash flows of AtheroGenics for the interim
periods. Certain footnote disclosures normally included in financial statements
prepared in accordance with generally accepted accounting principles have been
condensed or omitted from the interim financial statements as permitted by the
rules and regulations of the Securities and Exchange Commission. Interim results
are not necessarily indicative of results for the full year. The interim results
should be read in conjunction with the financial statements and notes thereto
included in the AtheroGenics' Registration Statement on Form S-1 (File No.
333-31140) (the "Registration Statement").

2.       NET LOSS PER SHARE AND PRO FORMA NET LOSS PER SHARE

         Net loss per share is computed using the weighted average number of
shares of common stock outstanding. Shares associated with stock options and
warrants and the convertible preferred stock are not included because they are
antidilutive.

         Pro forma net loss per share is computed using the weighted average
number of common shares outstanding, including pro forma effects of the
automatic conversion of outstanding redeemable convertible preferred stock into
shares of AtheroGenics' common stock effective upon the closing of AtheroGenics'
initial public offering (refer to Note 4) as if such conversion occurred on the
date of original issuance.

         The following is a reconciliation of the numerator and denominator of
basic and diluted and pro forma basic and diluted net loss per share amounts:

<TABLE>
<CAPTION>

                                                         Three Months Ended                  Six Months Ended
                                                              June 30,                           June 30,
                                                  ------------------------------      ------------------------------
                                                       2000              1999              2000              1999
                                                  ------------      ------------      ------------      ------------
<S>                                               <C>               <C>               <C>               <C>
Basic and diluted
     Net Loss ...............................     $ (3,083,213)     $ (2,569,057)     $ (6,478,006)     $ (5,319,392)
                                                  ============      ============      ============      ============
     Weighted average shares used in
     computing basic and diluted net loss
     per share ..............................        2,929,823         2,426,521         2,782,819         2,419,323
                                                  ============      ============      ============      ============

     Basic and diluted net loss per share ...     $      (1.05)     $      (1.06)     $      (2.33)     $      (2.20)
                                                  ------------      ------------      ------------      ------------

Pro forma basic and diluted:
     Shares used above ......................        2,929,823         2,426,521         2,782,819         2,419,323
  Pro forma adjustment to reflect weighted
     average effect of assumed conversion
     of preferred stock .....................       13,859,102         9,978,456        13,777,921         7,782,636
                                                  ------------      ------------      ------------      ------------
  Pro forma weighted average shares of
     common stock outstanding ...............       16,788,925        12,404,977        16,560,740        10,201,959
                                                  ============      ============      ============      ============
  Basic and diluted pro forma loss per
       share ................................     $       (.18)     $       (.21)     $       (.39)     $       (.52)
                                                  ============      ============      ============      ============
</TABLE>


                                       6
<PAGE>   7

3.       DEFERRED STOCK COMPENSATION

         During 1999, in connection with the grant of stock options to employees
and directors, AtheroGenics recorded non-cash deferred stock compensation of
$1.9 million, representing the difference between the fair value of common stock
on the dates such options were granted and the exercise prices. During the six
months ended June 30, 2000 AtheroGenics recorded additional deferred stock
compensation of $12.1 million in connection with grants of stock options
subsequent to December 31, 1999. These amounts are included as a reduction of
shareholders' equity and are being amortized over the vesting periods of the
individual options, generally four years, using the graded vesting method. The
graded vesting method provides for vesting of portions of the overall award at
interim dates and results in higher vesting in earlier years than straight-line
vesting. The fair value of AtheroGenics common stock for purposes of this
calculation was determined based on the business factors underlying the value of
common stock on the date such option grants were made. AtheroGenics recorded
amortization of deferred stock compensation of $85,480 in 1999. During the six
months ended June 30, 2000, AtheroGenics recorded a total of $3.9 million of
amortization of deferred stock compensation, as compared to $225 during the same
period in the prior year. At June 30, 2000, AtheroGenics had a total of $9.8
million remaining to be amortized over the vesting periods of the stock options.

4.       SUBSEQUENT EVENTS

         INITIAL PUBLIC OFFERING

         On August 8, 2000, AtheroGenics' Registration Statement was declared
effective by the Securities and Exchange Commission. Pursuant to the
Registration Statement, on August 9, 2000, AtheroGenics sold 6,000,000 shares of
its common stock at $8 per share. AtheroGenics received net proceeds of
approximately $43,200,000 from its initial public offering, after payment of
underwriting discounts and commissions and estimated offering expenses.

         The accompanying balance sheet as of June 30, 2000 does not reflect the
net proceeds of the AtheroGenics' initial public offering. Immediately prior to
the closing of the AtheroGenics' initial public offering on August 14, 2000, all
of the outstanding shares of the AtheroGenics' convertible preferred stock
automatically converted into 13,859,102 shares of common stock. Immediately
following the automatic conversion of the preferred stock, AtheroGenics filed an
amended and restated certificate of incorporation. Under the amended and
restated certificate of incorporation, AtheroGenics is authorized to issue
100,000,000 shares of common stock and 5,000,000 shares of preferred stock.
There currently are no shares of Preferred Stock issued and outstanding.


                                       7
<PAGE>   8

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

The following should be read with the financial statements and related footnotes
and Management's Discussion and Analysis of Results of Operations and Financial
Condition included in AtheroGenics' Registration Statement on Form S-1(File No.
333-31140). The results discussed below are not necessarily indicative of the
results to be expected in any future periods. The following discussion contains
forward-looking statements that are subject to risks and uncertainties which
could cause actual results to differ from the statements made.

OVERVIEW

         Since our operations began in 1994, we have been engaged in the
discovery and development of novel therapeutics for the treatment of acute and
chronic inflammatory diseases. Our lead product candidate, AGI-1067, is
currently in Phase II clinical trials for the treatment and prevention of
post-angioplasty restenosis.

         To date, we have devoted substantially all of our resources to research
and development. We have not derived any commercial revenues from product sales
and, excluding the effect of certain license fees of a non-recurring nature
received in connection with entering into an exclusive license agreement, we
expect to incur significant losses in most years prior to deriving any such
product revenue. We have incurred significant losses since we began operations
in 1994 and as of June 30, 2000 we had an accumulated deficit of $36.2 million.
There can be no assurance if or when we will become profitable. We expect to
continue to incur significant operating losses over the next several years as we
continue to incur increasing research and development costs. We expect that
losses will fluctuate from quarter to quarter and that such fluctuations may be
substantial. Our ability to achieve profitability depends upon our ability,
alone or with others, to complete the successful development of our product
candidates, to obtain required regulatory clearances, and to manufacture and
market our future products. In October 1999 we entered into an exclusive
licensing agreement with Schering-Plough covering our lead compound, AGI-1067.
Under terms of the agreement, Schering-Plough obtained exclusive worldwide
rights to AGI-1067 and related compounds. Schering-Plough is responsible for all
costs of development and commercialization. Schering-Plough paid us an initial
licensing fee and will pay additional fees upon achievement of specific
development, regulatory and commercial milestones.

RESULTS OF OPERATIONS

COMPARISON OF THE THREE MONTH PERIODS ENDED JUNE 30, 2000 AND 1999

Revenues

         Total revenues were $2.1 million for the three months ended June 30,
2000, compared to none in 1999. Revenues of $833,333 in 2000 were attributable
to licensing fees from the exclusive license agreement signed in October 1999
with Schering-Plough. This amount represents the earned portion of the $5.0
million initial license fee, which is being amortized over 18 months.


                                       8
<PAGE>   9

Research and development revenues related to such license agreement were $1.2
million for the three-month period ended June 30, 2000.

Expenses

         Research and Development. Research and development expenses were $2.7
million for the three months ended June 30, 2000, compared to $1.6 million for
the three months ended June 30, 1999. The increase of $1.1 million, or 69%,
reflects the continued expansion of our internal research and development
capabilities, higher costs associated with the AGI-1067 clinical trials and
pre-clinical costs related to our other product development programs.

         General and Administrative. General and administrative expenses were
$575,177 for the three months ended June 30, 2000, compared to $754,047 for the
three months ended June 30, 1999. The decrease of $178,870, or 24%, was
primarily due to lower consulting fees and travel costs. We expect that general
and administrative expenses will increase as we hire additional administrative
personnel to support continued growth of our research and development efforts
and incur additional costs related to being a public company, including
directors' and officers' insurance premiums, an investor relations program and
increased professional fees.

         Amortization of Deferred Stock Compensation. In 1999 and 2000, we
recorded non-cash deferred stock compensation totaling approximately $14.0
million for options granted with exercise prices below the deemed fair value for
financial reporting purposes of our common stock on their respective grant
dates. This deferred stock compensation is being amortized using the graded
vesting method. Amortization of deferred stock compensation was $2.0 million for
the three months ended June 30, 2000, compared to $225 for the three months
ended June 30, 1999. The increase is due to option grants made in the second
half of 1999 and the first half of 2000.

Net Interest Income (Expense)

         Net interest income was $136,532 for the three months ended June 30,
2000 as compared to net interest expense of $198,558 for the three months ended
June 30, 1999. The increase in net interest income was due to an increased level
of invested funds, as well as the elimination of interest expense related to a
bridge loan, which was converted to preferred stock in April 1999.

COMPARISON OF THE SIX MONTH PERIODS ENDED JUNE 30, 2000 AND 1999

Revenues

         Total revenues were $4.2 million for the six months ended June 30,
2000, compared to none in 1999. Revenues of $1.7 million in 2000 were
attributable to licensing fees from the exclusive license agreement signed in
October 1999 with Schering-Plough. This amount represents the earned portion of
the $5.0 million initial license fee, which is being amortized over 18 months.
Research and development revenues related to such license agreement were $2.5
million in for the six month period ended June 30, 2000.

Expenses

         Research and Development. Research and development expenses were $5.6
million for the six months ended June 30, 2000, compared to $3.8 million for the
six months ended June 30, 1999. The increase of $1.8 million, or 47%, reflects
the continued expansion of our internal


                                       9
<PAGE>   10

research and development capabilities, higher costs associated with the AGI-1067
clinical trials and pre-clinical costs related to our other product development
programs.

         General and Administrative. General and administrative expenses were
$1.4 million for the six months ended June 30, 2000, compared to $1.2 million
for the six months ended June 30, 1999. The increase of $180,360, or 15%, was
primarily due to increases in facility costs, personnel costs and professional
fees.

         Amortization of Deferred Stock Compensation. In 1999 and 2000, we
recorded non-cash deferred stock compensation totaling approximately $14.0
million for options granted with exercise prices below the deemed fair value for
financial reporting purposes of our common stock on their respective grant
dates. This deferred stock compensation is being amortized using the graded
vesting method. Amortization of deferred stock compensation was $4.0 million for
the six months ended June 30, 2000, compared to $225 for the six months ended
June 30, 1999.

Net Interest Income (Expense)

         Net interest income was $294,299 for the six months ended June 30, 2000
as compared to net interest expense of $320,801 for the six months ended June
30, 1999. The increase in net interest income was due to an increased level of
invested funds, as well as the elimination of interest expense related to the
bridge loan, which was converted to preferred stock in April 1999.

LIQUIDITY AND CAPITAL RESOURCES

         Since inception, we have financed our operations primarily through
private placements of preferred stock, which have resulted in net proceeds to us
of $39.2 million through June 30, 2000. We had cash and cash equivalents of $8.7
million at June 30, 2000, compared with $13.4 million at December 31, 1999.
Working capital at June 30, 2000 was $6.4 million, compared to $9.7 million at
December 31, 1999. Long-term debt was $130,085 at June 30, 2000 compared to
$61,854 for the year ending December 31, 1999. Long-term debt consists primarily
of capital equipment lease obligations.

         Net cash used in operating activities was $4.9 million for the six
months ended June 30, 2000, compared to $8.3 million for the six months years
ended June 30, 1999. The decrease in net cash used in 2000 compared to 1999
resulted principally from a greater use of funds for operating assets and
liabilities in 1999 than in 2000.

         Net cash used in investing activities was $726,204 for the six months
ended June 30, 2000, compared to $166,778 for the six months ended June 30,
1999. Net cash used in investing activities consisted primarily of equipment
purchases and leasehold improvements.

         Net cash provided by financing activities was $896,143 for the six
months ended June 30, 2000, compared to $9.7 million for the six months ended
June 30, 1999. Net cash provided by financing activities in 2000 consisted
primarily of proceeds from the exercise of preferred stock warrants and common
stock options. Net cash provided by financing activities in 1999 consisted
primarily of proceeds from the sale of preferred stock.


                                       10
<PAGE>   11

         Based upon the current status of our product development and
commercialization plans, we believe that our existing cash and cash equivalents,
together with the net proceeds from our initial public offering in August 2000,
will be adequate to satisfy our capital needs for at least the next 12 months.
However, our actual capital requirements will depend on many factors, including:

         -        the status of product development;

         -        the time and cost involved in conducting clinical trials and
                  obtaining regulatory approvals;

         -        filing, prosecuting and enforcing patent claims;

         -        competing technological and market developments; and

         -        our ability to market and distribute our future products and
                  establish new licensing agreements.


FORWARD-LOOKING STATEMENTS

         The Private Securities Litigation Reform Act of 1995 (the "Reform Act")
provides a safe harbor for forward-looking statements made by or on behalf of
AtheroGenics. AtheroGenics and its representatives may from time to time make
written or verbal forward-looking statements, including statements contained in
this report and other company filings with the Securities and Exchange
Commission and in our reports to our shareholders. Generally, the words
"believe," "expect," "intend," "estimate," "anticipate," "will" and similar
expressions identify forward-looking statements. All statements which address
operating performance, events or developments that we expect or anticipate will
occur in the future, including projections about our future results of
operations or our financial condition, our anticipated product commercialization
strategies, and anticipated trends in our business, are forward-looking
statements within the meaning of the Reform Act. The forward-looking statements
are and will be based on management's then current views and assumptions
regarding future events and operating performance, and speak only as of their
dates. The Company undertakes no obligation to publicly update or revise any
forward-looking statements, whether as a result of new information, future
events or otherwise.

         The following are some of the factors that could affect our financial
performance or could cause actual results to differ materially from those
expressed or implied in our forward-looking statements:

         -        AGI-1067 may fail in clinical trials

         -        Our ability to generate positive cash flow in light of our
                  history of operating losses

         -        Our ability to successfully develop our other product
                  candidates

         -        Our ability to commercialize our product candidates if we fail
                  to demonstrate adequately their safety and efficacy

         -        Possible delays in our clinical trials


                                       11
<PAGE>   12

         -        Our inability to predict whether or when we will obtain
                  regulatory approval to commercialize our product candidates or
                  the timing of any future revenue from these product candidates

         -        If Schering-Plough decides to terminate our exclusive license
                  agreement, we would lose access to their substantial
                  development, commercial and financial resources, which could
                  materially adversely affect our ability to develop and
                  commercialize AGI-1067

         -        The receipt and timing of milestone payments from
                  Schering-Plough is uncertain

         -        Our ability to protect adequately or enforce our intellectual
                  property rights or secure rights to third party patents

         -        The ability of our competitors to develop and market
                  anti-inflammatory products that are more effective, have fewer
                  side effects or are less expensive than our current or future
                  product candidates

         -        Third parties' failure to synthesize and manufacture our
                  product candidates could delay our clinical trials or hinder
                  our commercialization prospects

         -        Our ability to create sales, marketing and distribution
                  capabilities or enter into agreements with third parties to
                  perform these functions

         -        Our ability to attract, retain and motivate skilled personnel
                  and cultivate key academic collaborations

         -        If we need additional financing and cannot obtain it, we may
                  not be able to develop or market our products

         -        Our ability to obtain an adequate level of reimbursement or
                  acceptable prices for our products

         -        If plaintiffs bring product liability lawsuits against us, we
                  may incur substantial financial loss or may be unable to
                  obtain future product liability insurance at reasonable
                  prices, if at all, either of which could diminish our ability
                  to commercialize our future products

         The foregoing list of important factors is not exclusive.

ITEM 3. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

         Market risk represents the risk of loss that may impact our financial
position, operating results or cash flows due to changes in U.S. interest rates.
This exposure is directly related to our normal operating activities. Our cash,
cash equivalents and short-term investments are invested with high quality
issuers and are generally of a short-term nature. Interest rates payable on our
lease obligations are generally fixed. As a result, we do not believe that
near-term changes in interest rates will have a material effect on our future
results of operations.


                                       12
<PAGE>   13

                  PART II - OTHER INFORMATION


ITEM 1. LEGAL PROCEEDINGS

         None

ITEM 2. CHANGES IN SECURITIES AND USE OF PROCEEDS

         The effective date of the Registration Statement on Form S-1
(Registration No. 333-31140) filed under the Securities Act of 1933, as amended,
relating to the initial public offering of our common stock was August 8, 2000.
On the same date, we signed an underwriting agreement with Chase Securities
Inc., FleetBoston Robertson Stephens Inc., Adams, Harkness, & Hill, Inc. and
A.G. Edwards & Sons, Inc., the managing underwriters for the initial public
offering and the representatives of the underwriters named in the underwriting
agreement, for the initial public offering of 6,000,000 shares of our common
stock at an initial public offering price of $8.00 per share. The offering
commenced on August 9, 2000 and was closed on August 14, 2000. The initial
public offering resulted in gross proceeds of $48.0 million. We received net
proceeds of $43.2 million after deducting underwriting discounts of $3.4 million
and estimated offering expenses of $1.4 million.

         Concurrently with the closing of the initial public offering, the
13,859,102 outstanding shares of our Series A, B and C Preferred Stock were
automatically converted into 13,859,102 shares of common stock. As a result, we
no longer have any outstanding preferred stock.

         Because the initial public offering occurred after June 30, 2000, we
had not used any of the net proceeds from the offering through the end of the
period covered by this report on Form 10-Q. We expect that our use of proceeds
from the offering will conform to the intended use of proceeds as described in
our initial public offering prospectus dated August 9, 2000.

ITEM 3. DEFAULTS UPON SENIOR SECURITIES

         None

ITEM 4. SUBMISSION OF MATTERS TO A VOTE OF SECURITY HOLDERS

         None

ITEM 5. OTHER INFORMATION

         None


                                       13
<PAGE>   14

ITEM 6. EXHIBITS AND REPORTS ON FORM 8-K

         a.       Exhibits

<TABLE>
<CAPTION>
                  EXHIBIT
                  NUMBER            DESCRIPTION OF DOCUMENT
                  -------           -----------------------
                  <S>               <C>
                  3.1(+)            Amended and Restated Certificate of Incorporation
                  3.2(+)            Amended and Restated Bylaws
                  4.1(+)            Specimen Common Stock Certificate
                  27.1              Financial Data Schedule (for SEC use only)
</TABLE>

                  ---------------
                  (+) Filed with AtheroGenics' Registration Statement on Form
                  S-1, Registration No. 333- 31140, declared effective by the
                  Securities and Exchange Commission on August 8, 2000, and
                  incorporated herein by reference.

         b.       Reports on Form 8-K

                  No report on Form 8-K has been filed by AtheroGenics during
                  the quarter for which this report is filed.


                                       14
<PAGE>   15

                                   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.



                                ATHEROGENICS, INC.

Date: September 7, 2000.        By: /s/ RUSSELL M. MEDFORD, M.D., PH.D.
                                ------------------------------------------------
                                RUSSELL M. MEDFORD, M.D., PH.D.
                                President and Chief Executive Officer

Date: September 7, 2000.        By: /s/ MARK P. COLONNESE
                                ------------------------------------------------
                                MARK P. COLONNESE
                                Vice President of Finance and Administration and
                                Chief Financial Officer (Principal Accounting
                                and Financial Officer)


                                       15
<PAGE>   16

                                INDEX TO EXHIBITS

<TABLE>
<CAPTION>

EXHIBIT
NUMBER             DESCRIPTION OF DOCUMENT
-------            -----------------------
<S>                <C>
3.1(+)             Amended and Restated Certificate of Incorporation
3.2(+)             Amended and Restated Bylaws
4.1(+)             Specimen Common Stock Certificate
27.1               Financial Data Schedule (for SEC use only)
</TABLE>

         -----------------
         (+) Filed with AtheroGenics' Registration Statement on Form S-1,
         Registration No. 333-31140, declared effective by the Securities and
         Exchange Commission on August 8, 2000, and incorporated herein by
         reference.


                                       16