<Page>

                                    FORM 10Q
                                  UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549

              /X/ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d)
                     OF THE SECURITIES EXCHANGE ACT OF 1934
                For the quarterly period ended September 30, 2002

                                       OR

              / / TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d)
                     OF THE SECURITIES EXCHANGE ACT OF 1934
                      For the transition period from ___ to

                          Commission File Number 1-6549

                     American Science and Engineering, Inc.
             ------------------------------------------------------
             (Exact name of Registrant as specified in its charter)

          Massachusetts                                         04-2240991
-------------------------------                            -------------------
(State or other jurisdiction of                             (I.R.S. Employer
incorporation or organization)                             Identification No.)

  829 Middlesex Turnpike
  Billerica, Massachusetts                                     01821
---------------------------                                  ----------
(Address of principal executive offices)                     (Zip Code)

                                 (978) 262-8700
                              ---------------------
              (Registrant's telephone number, including area code)

      (Former name, former address and former fiscal year, if changed since
                                  last report)

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, 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

                                                   Outstanding at
          Class of Common Stock                    September 30, 2002
          ---------------------                    ------------------
          $.66 2/3 par value                         6,827,425

                               Page 1 of 29 Pages
                     The Exhibit Index is Located on Page 20

<Page>

             AMERICAN SCIENCE AND ENGINEERING, INC. AND SUBSIDIARIES
                         PART I - FINANCIAL INFORMATION
                           CONSOLIDATED BALANCE SHEETS
                                   (UNAUDITED)

Dollars in thousands

<Table>
<Caption>
                                                                    SEPTEMBER 30,
                                                                        2002        MARCH 31, 2002
                                                                    -------------   --------------
<S>           <C>                                                   <C>             <C>
ASSETS        Current assets:
              Cash and cash equivalents                             $      13,385   $        7,591
              Accounts receivable, net of allowances of $108 at
                September 30, 2002 and  $111 at March 31, 2002             10,359            7,216
              Unbilled costs and fees, net of allowances
                of $437 at September 30, 2002 and March 31, 2002            4,738            5,456
              Inventories                                                  20,114           21,013
              Deferred income taxes                                         2,475            2,475
              Prepaid expenses and other current assets                       500              685
                                                                    -------------   --------------
              Total current assets                                         51,571           44,436

              Non-current assets:
              Non-current deferred income taxes                               823              823
              Other assets                                                    154              204
              Patents and other intangibles, net of accumulated
                amortization of $392 at September 30, 2002 and
                $351 at March 31, 2002                                         74              115
              Property and equipment, net of accumulated
                depreciation of $16,425 at September 30, 2002
                and $15,366 at March 31, 2002                               3,852            4,663
                                                                    -------------   --------------

                                                                    $      56,474   $       50,241
                                                                    =============   ==============
</Table>

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

                                       -2-
<Page>

             AMERICAN SCIENCE AND ENGINEERING, INC. AND SUBSIDIARIES
                           CONSOLIDATED BALANCE SHEETS
                                   (UNAUDITED)
                                   (CONTINUED)

Dollars in thousands

<Table>
<Caption>
                                                                         SEPTEMBER 30,
                                                                             2002         MARCH 31, 2002
                                                                         -------------    --------------
<S>                   <C>                                                <C>              <C>
LIABILITIES &         Current liabilities:
STOCKHOLDERS'         Line of credit                                     $           -    $        9,319
INVESTMENT            Accounts payable                                           4,151             6,557
                      Accrued salaries and benefits                              1,556             1,577
                      Accrued warranty costs                                       585               196
                      Deferred revenue                                             934             1,030
                      Customer deposits                                          6,394             4,875
                      Accrued income taxes                                         768               763
                      Other current liabilities                                  1,511             1,783
                                                                         -------------    --------------
                      Total current liabilities                                 15,899            26,100
                                                                         -------------    --------------
                      Non-current liabilities:
                      Warrant liability                                          1,031                 -
                      Deferred revenue                                           1,000               691
                      Deferred compensation                                         98               109
                      Deferred rent                                                174               212
                                                                         -------------    --------------
                      Total non-current liabilities                              2,303             1,012
                                                                         -------------    --------------
                      Stockholders' investment:
                      Preferred stock, no par value
                        Authorized  - 100,000 shares
                        Issued - none                                                -                 -
                      Common stock, $.66-2/3 par value
                        Authorized - 20,000,000 shares
                        Issued 6,827,425 shares at September 30, 2002
                        and 5,549,478 shares at March 31, 2002                   4,551             3,699
                      Capital in excess of par value                            38,379            22,482
                      Accumulated deficit                                       (4,658)           (3,052)
                                                                         -------------    --------------
                      Total stockholders' investment                            38,272            23,129
                                                                         -------------    --------------
                                                                         $      56,474    $       50,241
                                                                         =============    ==============
</Table>

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

                                       -3-
<Page>

             AMERICAN SCIENCE AND ENGINEERING, INC. AND SUBSIDIARIES
                         PART I - FINANCIAL INFORMATION
                      CONSOLIDATED STATEMENTS OF OPERATIONS
                                   (UNAUDITED)

Dollars and shares in thousands, except per share amounts

<Table>
<Caption>
                                                     FOR THE THREE MONTHS ENDED           FOR THE SIX MONTHS ENDED
                                                   -------------------------------     -------------------------------
                                                     SEPT. 30,         SEPT. 30,         SEPT. 30,         SEPT. 30,
                                                       2002              2001              2002              2001
                                                   -------------     -------------     -------------     -------------
<S>                                                <C>               <C>               <C>               <C>
Net sales and contract revenues                    $      16,935     $      15,434     $      31,853     $      34,461
Cost of sales and contracts                               13,573            12,050            25,001            26,463
                                                   -------------     -------------     -------------     -------------
Gross profit                                               3,362             3,384             6,852             7,998

Expenses:
  Selling, general and administrative expenses             3,776             2,905             6,948             5,573
  Research and development                                 1,657             1,597             3,523             3,194
                                                   -------------     -------------     -------------     -------------
  Total expenses                                           5,433             4,502            10,471             8,767
                                                   -------------     -------------     -------------     -------------

Operating loss                                            (2,071)           (1,118)           (3,619)             (769)
                                                   -------------     -------------     -------------     -------------

Other income (expense):
  Interest expense                                             -              (121)              (86)             (243)
  Other, net                                               1,374               (46)            2,099              (116)
                                                   -------------     -------------     -------------     -------------
  Total other income (expense)                             1,374              (167)            2,013              (359)
                                                   -------------     -------------     -------------     -------------

Loss before income taxes                                    (697)           (1,285)           (1,606)           (1,128)

Benefit from income taxes                                      -              (488)                -              (430)
                                                   -------------     -------------     -------------     -------------

Net loss                                           $        (697)    $        (797)    $      (1,606)    $        (698)
                                                   =============     =============     =============     =============

Loss per share - Basic                             $       (0.10)    $       (0.16)    $       (0.25)    $       (0.14)
                                                   =============     =============     =============     =============
               - Diluted                           $       (0.10)    $       (0.16)    $       (0.25)    $       (0.14)
                                                   =============     =============     =============     =============

Weighted average shares - Basic                            6,818             5,030             6,395             5,026
                                                   =============     =============     =============     =============
                        - Diluted                          6,818             5,030             6,395             5,026
                                                   =============     =============     =============     =============
</Table>

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

                                       -4-
<Page>

             AMERICAN SCIENCE AND ENGINEERING, INC. AND SUBSIDIARIES
                      CONSOLIDATED STATEMENTS OF CASH FLOWS
                                   (UNAUDITED)

<Table>
<Caption>
Dollars in thousands                                             FOR THE SIX MONTHS ENDED
                                                              -------------------------------
                                                              SEPTEMBER 30,     SEPTEMBER 30,
                                                                  2002              2001
                                                              -------------     -------------
<S>                                                           <C>               <C>
Cash flows from operating activities:
Net loss                                                      $      (1,606)    $        (698)
Adjustments to reconcile net loss to net cash provided by
   (used for) operating activities:
   Depreciation and amortization                                      1,098             1,188
   Provisions for contract, inventory, accounts receivable
     and warranty reserves                                              896               106
   Change in fair value of warrants issued                           (2,087)                -
   Changes in assets and liabilities:
      Accounts receivable                                            (3,143)            1,245
      Unbilled costs and fees                                           718             4,776
      Inventories                                                       609               452
      Prepaid expenses, deposits and other assets                       235               271
      Accounts payable                                               (2,406)           (2,460)
      Accrued income taxes                                                5              (422)
      Customer deposits                                               1,519               289
      Deferred revenue                                                  213               (31)
      Accrued expenses and other current liabilities                   (296)           (1,439)
      Non-current liabilities                                           (49)              (38)
                                                              -------------     -------------
   Total adjustments                                                 (2,688)            3,937
                                                              -------------     -------------
Net cash provided by (used for) operating activities                 (4,294)            3,239
                                                              -------------     -------------

Cash flows from investing activities:
   Purchase of property and equipment                                  (246)             (378)
                                                              -------------     -------------
Net cash used for investing activities                                 (246)             (378)
                                                              -------------     -------------

Cash flows from financing activities:
   Borrowing under line of credit                                         -             1,500
   Repayments of line of credit                                      (9,319)                -
   Proceeds from issuance of common stock and warrants               18,423                 -
   Proceeds from exercise of stock options                            1,230                 3
                                                              -------------     -------------
Net cash provided by financing activities                            10,334             1,503
                                                              -------------     -------------

Net increase in cash and cash equivalents                             5,794             4,364
Cash and cash equivalents at beginning of period                      7,591             1,206
                                                              -------------     -------------
Cash and cash equivalents at end of period                    $      13,385     $       5,570
                                                              =============     =============

Supplemental disclosures of cash flow information:
   Interest paid                                              $         124     $         220
   Income taxes paid                                          $           -     $          15
Non-cash transactions:
   Issuance of stock and warrants in lieu of fees             $         382     $         191
</Table>

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

                                       -5-
<Page>

             AMERICAN SCIENCE AND ENGINEERING, INC. AND SUBSIDIARIES
           PREPARATION OF UNAUDITED CONSOLIDATED FINANCIAL STATEMENTS

   The consolidated financial statements included herein have been prepared by
   American Science and Engineering, Inc. (the Company) pursuant to the rules
   and regulations of the Securities and Exchange Commission, and the annual
   consolidated financial statements are subject to year end audit by
   independent public accountants. Certain information and footnote disclosures
   normally included in financial statements prepared in accordance with
   generally accepted accounting principles have been omitted pursuant to such
   rules and regulations. The Company believes, however, that the disclosures
   are adequate to make the information presented not misleading. It is
   suggested that these consolidated financial statements be read in conjunction
   with the consolidated financial statements and the notes thereto included in
   the Company's latest annual report on Form 10-K.

   The consolidated financial statements, in the opinion of management, include
   all adjustments necessary, consisting solely of normal recurring adjustments,
   to present fairly the Company's financial position, results of operations and
   cash flows. These results are not necessarily indicative of the results to be
   expected for the entire year.

   NOTES TO CONSOLIDATED FINANCIAL STATEMENTS (UNAUDITED)

1.   NATURE OF OPERATIONS AND SIGNIFICANT ACCOUNTING POLICIES
     The Company is engaged in the development and manufacture of sophisticated
     X-ray inspection systems for critical detection and security screening
     solutions for sale primarily to U.S. and foreign government agencies. The
     Company has only one reporting segment, X-ray screening products.

     The significant accounting policies followed by the Company and its
     Subsidiaries in preparing its consolidated financial statements are set
     forth in Note 1 to the consolidated financial statements included in its
     Form 10-K for the year ended March 31, 2002. The Company has made no
     changes to these policies during this quarter.

     NEW ACCOUNTING PRONOUNCEMENTS
     In April 2002, the Financial Accounting Standards Board (FASB) issued
     Statement of Financial Accounting Standards No. 145, "Rescission of FASB
     Statements No. 4, 44, and 64, Amendment of FASB Statement No. 13, and
     Technical Corrections" (FAS 145). This statement eliminates the requirement
     that gains and losses from the extinguishments of debt be aggregated and,
     if material, classified as an extraordinary item, net of the related income
     tax effect. However, an entity would not be prohibited from classifying
     such gains and losses as extraordinary items so long as they are both
     unusual in nature and infrequent in occurrence. This provision of FAS 145
     will be effective for the Company as of the beginning of fiscal year 2004.
     This statement also amends FAS 13, "Accounting for Leases" and certain
     other authoritative pronouncements to make technical corrections or
     clarifications. FAS 145 will be effective related to the amendment of FAS
     13 for all transactions occurring after May 15, 2002. All other provisions
     of FAS 145 will be effective for financial statements issued after May 15,
     2002. The Company is currently evaluating the impact of implementing FAS
     145.

     In July 2002, the FASB issued Statement of Financial Accounting Standards
     No. 146, "Accounting for Costs Associated with Exit or Disposal Activities"
     (FAS 146), which nullifies Emerging Issues Task Force (EITF) Issue No.
     94-3, "Liability Recognition for Certain Employee Termination Benefits and
     Other Costs to Exit an Activity (including Certain Costs Incurred in a
     Restructuring)." FAS 146 requires a liability for a cost associated with an
     exit or disposal activity be recognized and measured initially at its fair
     value in the period in which the liability is incurred. If fair value
     cannot be reasonably estimated, the liability shall be recognized initially
     in the period in which fair value can be reasonably estimated. The
     provisions of FAS 146 will be effective for the Company prospectively for
     exit or disposal activities initiated after December 31, 2002; however,
     this standard is not expected to have a significant impact.

                                       -6-
<Page>

     In October 2001, the FASB issued FAS No. 144, "Accounting for the
     Impairment or Disposal of Long Lived Assets" which supercedes FAS No. 121,
     "Accounting for the Impairment of Long-lived Assets and for Long-lived
     Assets to be Disposed of" and provisions of APB Opinion No. 30 "Reporting
     the Results of Operations-Reporting the Effects of Disposal of a Segment of
     a Business, and Extraordinary, Unusual and Infrequently Occurring Events
     and Transactions", for the disposal of segments of a business. The
     statement creates one accounting model, based on the framework established
     in FAS No. 121, to be applied to all long-lived assets including
     discontinued operations. FAS No. 144 was effective for the Company on April
     1, 2002 and will be applied prospectively.

2.   INVENTORIES

<Table>
<Caption>
             Inventories consisted of: (Dollars in         September 30,
             thousands)                                        2002         March 31, 2002
                                                           -------------    --------------
             <S>                                           <C>              <C>
             Raw materials and completed sub-assemblies    $      10,304    $       10,483
             Work in process                                       6,535             7,981
             Finished goods                                        3,275             2,549
                                                           -------------    --------------
             Total                                         $      20,114    $       21,013
                                                           =============    ==============
</Table>

3.   INCOME PER COMMON AND COMMON EQUIVALENT SHARE
     Basic earnings per common share is computed by dividing net income by the
     weighted average number of shares of common stock outstanding during the
     period. Diluted earnings per share includes the dilutive impact of options
     and warrants using the average share price of the Company's common stock
     for the period. For the quarter and six months ended September 30, 2002 and
     2001, common stock equivalents of 230,100 and 450,906 and 100,000 and
     67,000, respectively, are excluded from diluted earnings per share, as
     their effect is anti-dilutive.

<Table>
<Caption>
    Earnings Per Share                       Three Months Ended                   Six Months Ended
    ------------------                --------------------------------   ---------------------------------
    (in thousands except per share    Sept. 30, 2002    Sept. 30, 2001   Sept. 30, 2002     Sept. 30, 2001
    amounts)                          --------------    --------------   --------------     --------------

    <S>                               <C>               <C>               <C>               <C>
    BASIC

    Net loss                          $        (697)    $        (797)    $      (1,606)    $         (698)
                                      -------------     -------------     -------------     --------------
    Weighted average shares                   6,818             5,030             6,395              5,026
                                      -------------     -------------     -------------     --------------
    Basic loss per share              $       (0.10)    $       (0.16)    $       (0.25)    $        (0.14)
                                      -------------     -------------     -------------     --------------
    DILUTED
    Net loss                          $        (697)    $        (797)    $      (1,606)    $         (698)
                                      -------------     -------------     -------------     --------------
    Weighted average shares                   6,818             5,030             6,395              5,026
                                      -------------     -------------     -------------     --------------
    Effect of stock options and
    warrants                                      -                 -                 -                  -
                                      -------------     -------------     -------------     --------------
    Weighted average shares, as
    adjusted                                  6,818             5,030             6,395              5,026
                                      -------------     -------------     -------------     --------------
    Diluted loss per share            $       (0.10)    $       (0.16)    $       (0.25)    $        (0.14)
                                      =============     =============     =============     ==============
</Table>

                                       -7-
<Page>

4.   BORROWINGS

     On November 30, 2000, the Company signed two credit agreements with HSBC
     Bank USA ("HSBC"). The first agreement was for a $10 million domestic
     revolving credit facility to support the Company's routine working capital
     and standby letter of credit needs. The second was a $30 million export
     credit and security agreement, guaranteed by the Export-Import Bank of the
     United States ("Ex-Im"), to support the Company's overseas contract, trade
     finance and working capital needs. The credit facility bears an interest
     rate of the HSBC Bank USA prime rate or LIBOR plus 2.0% at the Company's
     option.

     On February 14, 2002, these credit agreements were amended to increase the
     domestic revolving credit facility to $20 million and to reduce the export
     credit and security agreement to $20 million. The domestic revolving credit
     facility as amended provides for maximum borrowings in an amount up to the
     lower of: (a) the sum of 85% of eligible domestic accounts receivable plus
     the lower of: (i) 40% of eligible raw materials and work-in-process
     inventory; or; (ii) $5 million, or; (b) $20 million. The export credit and
     security agreement as amended provides for maximum borrowings in an amount
     up to the lower of: (a) 90% of eligible international billed and unbilled
     accounts receivable, or; (b) $20 million. The agreements expire on November
     30, 2002.

     At September 30, 2002, there were no borrowings outstanding against this
     facility and $4.5 million in letters of credit were in effect against this
     credit facility. The Company's credit facility restricts the payment of
     dividends, except in shares of the Company's stock, without consent of the
     bank and requires the Company to meet certain financial covenants. As of
     September 30, 2002, the Company was not in compliance with one of these
     financial covenants, but has obtained a waiver from the bank for this
     non-compliance for the second quarter.

5.   PRIVATE PLACEMENT OFFERING
     On May 28, 2002, the Company closed on a private placement offering of
     common stock and warrants. A total of 1,115,000 shares were sold to
     accredited investors at a price of $17.64 each. In addition, warrants to
     purchase an additional 295,475 shares of common stock at a price of $23.52
     were issued. Proceeds to the Company approximated $18.4 million, net of
     approximately $1.3 million of issuance cost. The warrants were immediately
     vested and have a five-year life expiring in May of 2007. Due to certain
     conversion features of these warrants which provide for cash settlement
     under limited circumstances, in accordance with EITF 00-19, the potential
     cash liability, representing the fair value of the warrants, was recorded
     as a liability on the balance sheet at May 28, 2002 and the "mark to
     market" change in the warrants value at September 30, 2002 of $1,364,000
     was recorded as other income for the period. The liability of $1,031,000
     associated with the warrants is recorded as a non-current liability on the
     September 30, 2002 balance sheet. The fair market value of the warrants was
     determined using the Black Scholes pricing model and an assumed volatility
     of 72% and interest rate of 5%.

                                       -8-
<Page>

             AMERICAN SCIENCE AND ENGINEERING, INC. AND SUBSIDIARIES
                MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL
                       CONDITION AND RESULTS OF OPERATIONS

     ITEM 2 - RESULTS OF OPERATIONS
     Net sales and contract revenues in the second quarter increased by
     $1,501,000 (10%) in comparison to the corresponding period a year ago and
     increased by $2,017,000 (14%) compared to the first quarter of fiscal 2003.
     The increase in revenues from the prior quarter is due to increased sales
     of the Company's cargo products and field service revenues partially offset
     by lower sales of the Company's parcel products. The reduced level of
     revenues from parcel products is partially attributable to the record
     parcel product revenues recorded in the prior quarter.

     Net sales and contract revenues for the six month period ended September
     30, 2002 decreased by $2,608,000 (8%) compared to the corresponding period
     a year ago. This decrease in revenues from the prior year is due to reduced
     volumes in cargo products and field services revenues offset somewhat by a
     significant increase in the Company's parcel products revenues.

     For the second quarter, cost of sales and contracts increased to
     $13,573,000 from $12,050,000 in the corresponding period a year ago. Cost
     of sales and contracts represented 80% of revenues versus 78% for the
     corresponding period last year and 77% for the first quarter of fiscal year
     2003. The cost of sales as a percentage of revenue in the current quarter
     increased from the corresponding period last year due to the lower margins
     on certain cargo projects recorded on a percentage of completion basis in
     addition to charges to cost of sales in the current quarter related to the
     establishment of reserves for excess cargo inventories.

     Cost of sales and contracts for the six month period ended September 30,
     2002 decreased by $1,462,000 (6%) compared to the first six months of the
     prior year. This decrease is attributable to the decrease in revenues noted
     above offset somewhat by the lower margins on certain cargo projects and
     the establishment of reserves for excess cargo inventories in the second
     quarter of the current fiscal year.

     Selling, general and administrative expenses of $3,776,000 for the second
     quarter were higher by 30% compared to the corresponding period last year
     and higher by 19% compared to the first quarter of fiscal 2003. As a
     percent of sales, selling, general and administrative expenses were 22% of
     revenues in the current quarter compared to 19% of revenues for the
     corresponding period a year ago and 21% for the first quarter of fiscal
     year 2003. The increased costs in the quarter were due primarily to higher
     insurance and trade show expenses offset in part by lower legal expenses in
     the quarter.

     Selling, general and administrative expenses of $6,948,000 for the first
     six months of fiscal year 2003 increased by 25% from the selling, general
     and administrative expenses of $5,573,000 reported during the first six
     months of fiscal year 2002. The increased costs were due primarily to
     higher insurance, trade shows, bid and proposal support and additional
     personnel in critical areas.

     Company funded research and development expenses of $1,657,000 for the
     second quarter increased by $60,000 (4%) compared to the corresponding
     period last year and decreased by $209,000 or 11% from the first quarter of
     fiscal year 2003. The current quarter expenditures continue to be
     significant as the Company continues to focus on new product initiatives
     and improvements to address the demands of increased national security
     needs.

                                       -9-
<Page>

     Research and development expenses for the six month period ended
     September 30, 2002 were $3,523,000, or 10% above the $3,194,000 incurred in
     the same period in the prior year. The additional expense is due to the
     Company's continued commitment to find and develop new product initiatives
     to address the demands of increased national security needs offset somewhat
     by the reallocation of engineering resources to meet the requirements of
     increased bidding and proposal activities.

     As part of the private equity placement during the first quarter of 2003,
     the Company issued 295,475 warrants. Due to certain conversion features of
     these warrants, that provide cash settlement in certain instances, a
     liability equal to the Black-Scholes valuation of the warrants at the deal
     close was recorded on the Company's balance sheet. At September 30, 2002,
     these warrants were "marked to market" using Black-Scholes and the change
     in the valuation of the warrants of $1,364,000 was recorded as a credit to
     other income (expense) in the quarter. During the first quarter of this
     fiscal year, this calculation generated a $723,000 credit to other income
     (expense).

     The potential tax benefits on losses incurred in the first and second
     quarter of fiscal year 2003 have been fully reserved against due to the
     uncertainty as to whether additional loss carryforwards may ultimately be
     realized. In assessing the realizibility of deferred tax assets, management
     considers whether it is more likely than not that some portion or all of
     the deferred tax assets will not be realized. Although realization is not
     assured, the Company expects that deferred tax assets of $3.3 million, net
     of valuation allowance, at September 30, 2002 will be realized through
     future earnings. Accordingly, the Company believes that no valuation
     allowance is required for the remaining deferred tax assets. In fiscal year
     2002, the Company recorded a tax benefit of $488,000 after having
     recognized a $58,000 tax provision in the first quarter.

     The Company incurred a net loss of $697,000 during the second quarter of
     fiscal year 2003 as compared to a net loss of $797,000 in the second
     quarter of fiscal year 2002. During the first six months of fiscal year
     2003 the Company reported a loss of $1,606,000 as compared to a loss of
     $698,000 for the same period in the prior year. The significant factors
     contributing to these results are noted in the above sections.

     LIQUIDITY AND CAPITAL RESOURCES

     On May 28, 2002, the Company closed on a private placement offering of
     common stock and warrants. A total of 1,115,000 shares were sold to
     accredited investors at a price of $17.64 each. In addition, warrants to
     purchase an additional 295,475 shares of common stock at a price of $23.52
     were issued. These warrants have a five-year life expiring in May of 2007.
     Proceeds to the Company approximated $18.4 million. The proceeds from this
     private placement offering have been and are being utilized for general
     corporate purposes including debt repayment, capital expenditures, and
     investments in product development and working capital needs.

     Cash and cash equivalents increased by $5,794,000 to $13,385,000 at
     September 30, 2002 compared to $7,591,000 at March 31, 2002. This increase
     in cash and cash equivalents was primarily due to proceeds received from
     the private equity placement and stock option exercises offset by the
     repayment of the line of credit and increases in accounts receivable and
     decreases in certain liabilities. Working capital increased by $17,336,000
     (95%) since March 31, 2002, increasing from $18,336,000 to $35,672,000 at
     the end of the first quarter due primarily to the stock and option proceeds
     received.

     On November 30, 2000, the Company signed two credit agreements with HSBC
     Bank USA ("HSBC"). The first agreement was for a $10 million domestic
     revolving credit facility to support the Company's routine

                                      -10-
<Page>

     working capital and standby letter of credit needs. The second was a $30
     million export credit and security agreement, guaranteed by the
     Export-Import Bank of the United States ("Ex-Im"), to support the Company's
     overseas contract, trade finance and working capital needs. The credit
     facility bears an interest rate of the HSBC Bank USA prime rate or LIBOR
     plus 2.0% at the Company's option.

     On February 14, 2002, these credit agreements were amended to increase the
     domestic revolving credit facility to $20 million and to reduce the export
     credit facility to $20 million. The domestic revolving credit facility as
     amended provides for maximum borrowings in an amount up to the lower of:
     (a) the sum of 85% of eligible domestic accounts receivable plus the lower
     of: (i) 40% of eligible raw materials and work-in-process inventory; or;
     (ii) $5 million, or; (b) $20 million. The export credit and security
     agreement as amended provides for maximum borrowings in an amount up to the
     lower of: (a) the sum of 90% of eligible international billed and unbilled
     accounts receivable, or; (b) $20 million. The agreements expire on
     November 30, 2002.

     The Company currently plans on refinancing either under the same agreement
     with HSBC or a similar agreement with a new facility; however, there can be
     no assurance that HSBC will renew the credit agreements or that alternative
     financing can be obtained. As discussed above, the Company has paid off the
     amounts outstanding under the domestic credit facilities and management
     believes the Company's working capital requirements through March 31, 2003
     can be met without the line of credit. In addition, to the extent the
     Company's credit facility is not renewed, it would preclude the Company
     from obtaining financing through its current secured export credit and
     security agreement which could negatively impact the Company's ability to
     support international sales. However, management believes the Company's
     planned level of sales in 2003 can be achieved without access to export
     credit.

     At September 30, 2002, there were no borrowings outstanding against this
     facility and $4.5 million in letters of credit were in effect against these
     credit facilities. The Company's credit facility restricts the payment of
     dividends, except in shares of the Company's stock, without consent of the
     bank and requires the Company to meet certain financial covenants. As of
     September 30, 2002, the Company was not in compliance with one of these
     financial covenants, but has obtained a waiver from the bank for this
     non-compliance.

     NEW ACCOUNTING PRONOUNCEMENTS:
     In April 2002, the Financial Accounting Standards Board (FASB) issued
     Statement of Financial Accounting Standards No. 145, "Rescission of FASB
     Statements No. 4, 44, and 64, Amendment of FASB Statement No. 13, and
     Technical Corrections" (FAS 145). This statement eliminates the requirement
     that gains and losses from the extinguishments of debt be aggregated and,
     if material, classified as an extraordinary item, net of the related income
     tax effect. However, an entity would not be prohibited from classifying
     such gains and losses as extraordinary items so long as they are both
     unusual in nature and infrequent in occurrence. This provision of FAS 145
     will be effective for the Company as of the beginning of fiscal year 2004.
     This statement also amends FAS 13, "Accounting for Leases" and certain
     other authoritative pronouncements to make technical corrections or
     clarifications. FAS 145 will be effective related to the amendment of FAS
     13 for all transactions occurring after May 15, 2002. All other provisions
     of FAS 145 will be effective for financial statements issued after May 15,
     2002. The Company is currently evaluating the impact of implementing FAS
     145.

     In July 2002, the FASB issued Statement of Financial Accounting Standards
     No. 146, "Accounting for Costs Associated with Exit or Disposal Activities"
     (FAS 146), which nullifies Emerging Issues Task Force (EITF) Issue No.
     94-3, "Liability Recognition for Certain Employee Termination Benefits and
     Other Costs to Exit an

                                      -11-
<Page>

     Activity (including Certain Costs Incurred in a Restructuring)." FAS 146
     requires a liability for a cost associated with an exit or disposal
     activity be recognized and measured initially at its fair value in the
     period in which the liability is incurred. If fair value cannot be
     reasonably estimated, the liability shall be recognized initially in the
     period in which fair value can be reasonably estimated. The provisions of
     FAS 146 will be effective for the Company prospectively for exit or
     disposal activities initiated after December 31, 2002; however, this
     standard is not expected to have a significant impact.

     In October 2001, the FASB issued FAS No. 144, "Accounting for the
     Impairment or Disposal of Long Lived Assets" which supercedes FAS No. 121,
     "Accounting for the Impairment of Long-lived Assets and for Long-lived
     Assets to be Disposed of" and provisions of APB Opinion No. 30 "Reporting
     the Results of Operations-Reporting the Effects of Disposal of a Segment of
     a Business, and Extraordinary, Unusual and Infrequently Occurring Events
     and Transactions", for the disposal of segments of a business. The
     statement creates one accounting model, based on the framework established
     in FAS No. 121, to be applied to all long-lived assets including
     discontinued operations. FAS No. 144 was effective for the Company on April
     1, 2002 and will be applied prospectively.

     ITEM 4 - CONTROLS AND PROCEDURES

     Within the 90-day period prior to the date of this report, we carried out
     an evaluation, under the supervision and with the participation of our
     management, including our Chief Executive Officer and Chief Financial
     Officer, of the effectiveness of the design and operation of our disclosure
     controls and procedures pursuant to Rule 13a-14(c) and 15d-14(c) of the
     Securities Exchange Act of 1934. Based upon that evaluation, our Chief
     Executive Officer and our Chief Financial Officer concluded that our
     disclosure controls and procedures are effective for gathering, analyzing
     and disclosing the information we are required to disclose in reports filed
     under such Act.

     There have been no significant changes in our internal controls or in other
     factors, which could significantly affect internal controls subsequent to
     the date that the Company carried out its evaluation.

     Part II - Other Information

     ITEM 1 - LEGAL PROCEEDINGS
     The United States Court of Appeals for the Federal Circuit in Washington,
     D.C., in a decision issued December 29, 1999, ruled that American Science &
     Engineering, may pursue a patent infringement claim against Vivid
     Technologies which produces X-ray detection devices used in baggage
     scanning equipment. The Appeals Court overturned a 1998 decision in Vivid's
     favor by the Massachusetts Federal District Court. The lawsuit, filed by
     Vivid Technologies in May 1996, concerns whether Vivid's X-ray detection
     devices infringed on the Company's patent. The District Court had ruled
     that the Company could not assert a claim that Vivid's devices infringed on
     the Company's patent. The Appeals Court also reversed the district court's
     finding on summary judgment that Vivid did not infringe on the Company's
     patent, as well as the district court's denial of the Company's request for
     discovery to oppose Vivid's summary judgment motion. Discovery is now
     proceeding.

     In September 1998, the Company filed suit against EG&G Astrophysics
     Research Corp. ("EG&G") in U.S. District Court in Massachusetts alleging
     that EG&G infringed on at least two patents owned by the Company and that
     EG&G has misappropriated certain trade secrets of the Company. In February
     1999, the Company

                                      -12-
<Page>

     filed a related action in the same court against the U.S. Customs Service
     ("Customs") alleging that Customs had either misappropriated the Company's
     trade secrets or facilitated their misappropriation by EG&G and that
     Customs had improperly entered into a contract with EG&G for the
     acquisition of a product functionally equivalent to MobileSearch(TM) X-ray
     inspection system. In May 1999, the Court held a hearing on the Company's
     motion for a preliminary injunction against both Customs and EG&G
     prohibiting further performance of the contested contract and preventing
     EG&G from utilizing the Company's trade secrets. In August 1999, the Court
     issued a ruling denying the request for the preliminary injunction. In
     December 1999, EG&G filed a motion for summary judgment that EG&G did not
     misappropriate the Company's trade secrets and in March 2000 EG&G filed a
     motion for summary judgment that EG&G did not infringe the Company's
     patents. In February 2001, the court denied EG&G's and the Company's
     motions for summary judgment. The Company is continuing to pursue its
     claims against EG&G, but the suit against U.S. Customs Service has been
     dismissed.

     In a related matter, EG&G filed a request with the U.S. Patent and
     Trademark Office ("USPTO") for re-examination of the two patents that
     currently are at issue in the patent infringement action described above.
     The Company filed oppositions to the re-examination requests and was
     advised by the USPTO that the Company's MobileSearch X-ray inspection
     patent was upheld in all material respects. The Company was also advised by
     the USPTO that the Company's patent on its Z(R) Backscatter X-ray
     inspection technology has been upheld in all material respects.

     The Company is also subject to various legal proceedings and claims that
     arise in the ordinary course of business. The Company currently believes
     that resolving these matters will not have a material adverse impact on its
     financial condition or results of operations.

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

At the special meeting held in lieu of the annual meeting of Stockholders of the
Company held on September 19, 2002, the stockholders of the Company (1) elected
William E. Odom, Roger P. Heinisch, Hamilton W. Helmer, Donald J. McCarren,
Ralph S. Sheridan and Carl W. Vogt as directors of the Company to hold office
for a one-year term and no other nominations were made; and (2) approved an
amendment to adopt the Company's 2002 Combination Stock Option Plan. The votes
were as follows:

<Table>
<Caption>
                                                                            Votes
                                                                         Withheld or
                                                           Votes For       Opposed        Abstentions
                                                           ---------     -----------      -----------
<S>                                                        <C>             <C>                 <C>
(1) Election of Directors:

William E. Odom                                            5,742,384          56,581

Roger P. Heinisch                                          5,742,384          56,581

Hamilton W. Helmer                                         5,742,384          56,581

Donald J. McCarren                                         5,742,384          56,581

Ralph S. Sheridan                                          4,498,479       1,096,986

Carl W. Vogt                                               5,742,330          56,635

2) Approval of the 2002 Combination Stock Option Plan      4,168,098       1,605,855           25,012
</Table>

                                      -13-
<Page>

ITEM 6 - EXHIBITS AND REPORTS ON FORM 8-K

(a)  EXHIBITS

10 Employment agreement between the Company and Ralph S. Sheridan, dated
July 11, 2002

99.1 Certification of Chief Executive Officer pursuant to 18 U.S.C. Section
1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002

99.2 Certification of Chief Financial Officer pursuant to 18 U.S.C. Section
1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002

(b)  REPORTS ON FORM 8-K

A report on Form 8-K was filed on July 19, 2002 announcing the change of
auditors from Arthur Andersen to PricewaterhouseCoopers LLP.

The information required by Exhibit Item 11 (Statement re: Computation of Income
per Common and Common Equivalent Share) may be found in Footnote No. 3 on
Page 7.

                                      -14-
<Page>

SIGNATURES

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


                                        AMERICAN SCIENCE AND ENGINEERING, INC.
                                         (Registrant)


     Date   November 14, 2002           /s/ Paul Theodore Owens
                                        --------------------------------------
                                        Paul Theodore Owens
                                        Interim Chief Financial Officer

SAFE HARBOR STATEMENT
THE FOREGOING 10-Q CONTAINS STATEMENTS CONCERNING THE COMPANY'S FINANCIAL
PERFORMANCE AND BUSINESS OPERATIONS WHICH MAY BE CONSIDERED "FORWARD-LOOKING"
UNDER APPLICABLE SECURITIES LAWS.

THE COMPANY WISHES TO CAUTION READERS OF THIS FORM 10-Q THAT ACTUAL RESULTS
MIGHT DIFFER MATERIALLY FROM THOSE PROJECTED IN ANY FORWARD-LOOKING STATEMENTS.

FACTORS WHICH MIGHT CAUSE ACTUAL RESULTS TO DIFFER MATERIALLY FROM THOSE
PROJECTED IN THE FORWARD-LOOKING STATEMENTS CONTAINED HEREIN INCLUDE THE
FOLLOWING: SIGNIFICANT REDUCTIONS OR DELAYS IN PROCUREMENTS OF THE COMPANY'S
SYSTEMS BY THE UNITED STATES GOVERNMENT; DISRUPTION IN THE SUPPLY OF ANY
SOLE-SOURCE COMPONENT INCORPORATED INTO THE COMPANY'S PRODUCTS (OF WHICH THERE
ARE SEVERAL); LITIGATION SEEKING TO RESTRICT THE USE OF INTELLECTUAL PROPERTY
USED BY THE COMPANY; POTENTIAL PRODUCT LIABILITY CLAIMS AGAINST THE COMPANY;
GLOBAL POLITICAL TRENDS AND EVENTS WHICH AFFECT PUBLIC PERCEPTION OF THE THREAT
PRESENTED BY DRUGS, EXPLOSIVES AND OTHER CONTRABAND; THE ABILITY OF GOVERNMENTS
AND PRIVATE ORGANIZATIONS TO FUND PURCHASES OF THE COMPANY'S PRODUCTS TO ADDRESS
SUCH THREATS; AND THE POTENTIAL INSUFFICIENCY OF COMPANY RESOURCES, INCLUDING
HUMAN RESOURCES, CAPITAL, PLANT AND EQUIPMENT AND MANAGEMENT SYSTEMS, TO
ACCOMMODATE ANY FUTURE GROWTH. THESE AND CERTAIN OTHER FACTORS WHICH MIGHT CAUSE
ACTUAL RESULTS TO DIFFER MATERIALLY FROM THOSE PROJECTED ARE MORE FULLY SET
FORTH UNDER THE CAPTION "FORWARD-LOOKING INFORMATION AND FACTORS AFFECTING
FUTURE PERFORMANCE" IN THE COMPANY'S REGISTRATION STATEMENT ON FORM 10-K.


                                      -15-
<Page>

                  CERTIFICATION OF PRINCIPAL EXECUTIVE OFFICER
                            SECTION 302 CERTIFICATION

I, Ralph S. Sheridan, certify that:

1. I have reviewed this quarterly report on Form 10-Q of American Science and
Engineering, Inc.;

2. Based on my knowledge, this quarterly report does not contain any untrue
statement of a material fact or omit to state a material fact necessary to make
the statements made, in light of the circumstances under which such statements
were made, not misleading with respect to the period covered by this quarterly
report;

3. Based on my knowledge, the financial statements, and other financial
information included in this quarterly report, fairly present in all material
respects the financial condition, results of operations and cash flows of the
registrant as of, and for, the periods presented in this quarterly report;

4. The registrant's other certifying officer and I are responsible for
establishing and maintaining disclosure controls and procedures (as defined in
Exchange Act Rules 13a-14 and 15d-14) for the registrant and we have:

     a) Designed such disclosure controls and procedures to ensure that material
information relating to the registrant, including its consolidated subsidiaries,
is made known to us by others within those entities, particularly during the
period in which this quarterly report is being prepared;

     b) Evaluated the effectiveness of the registrant's disclosure controls and
procedures as of a date within 90 days prior to the filing date of this
quarterly report (the "Evaluation Date"); and

     c) Presented in this quarterly report our conclusions about the
effectiveness of the disclosure controls and procedures based on our evaluation
as of the Evaluation Date;

5. The registrant's other certifying officer and I have disclosed, based on our
most recent evaluation, to the registrant's auditors and the audit committee of
registrant's board of directors (or persons performing the equivalent function):

     a) All significant deficiencies in the design or operation of internal
controls which could adversely affect the registrant's ability to record,
process, summarize and report financial data and have identified for the
registrant's auditors any material weaknesses in internal controls; and

     b) Any fraud, whether or not material, that involves management or other
employees who have a significant role in the registrant's internal controls; and

6. The registrant's other certifying officer and I have indicated in this
quarterly report whether or not there were significant changes in internal
controls or in other factors that could significantly affect


                                      -16-
<Page>

internal controls subsequent to the date of our most recent evaluation,
including any corrective actions with regard to significant deficiencies and
material weaknesses.

Date: November 14, 2002

/s/ Ralph S. Sheridan
---------------------------
Ralph S. Sheridan
President and Chief Executive Officer


                                      -17-
<Page>


                  CERTIFICATION OF PRINCIPAL FINANCIAL OFFICER
                            SECTION 302 CERTIFICATION

I, Paul Theodore Owens, certify that:

1. I have reviewed this quarterly report on Form 10-Q of American Science and
Engineering, Inc.;

2. Based on my knowledge, this quarterly report does not contain any untrue
statement of a material fact or omit to state a material fact necessary to make
the statements made, in light of the circumstances under which such statements
were made, not misleading with respect to the period covered by this quarterly
report;

3. Based on my knowledge, the financial statements, and other financial
information included in this quarterly report, fairly present in all material
respects the financial condition, results of operations and cash flows of the
registrant as of, and for, the periods presented in this quarterly report;

4. The registrant's other certifying officer and I are responsible for
establishing and maintaining disclosure controls and procedures (as defined in
Exchange Act Rules 13a-14 and 15d-14) for the registrant and we have:

     a) Designed such disclosure controls and procedures to ensure that material
information relating to the registrant, including its consolidated subsidiaries,
is made known to us by others within those entities, particularly during the
period in which this quarterly report is being prepared;

     b) Evaluated the effectiveness of the registrant's disclosure controls and
procedures as of a date within 90 days prior to the filing date of this
quarterly report (the "Evaluation Date"); and

     c) Presented in this quarterly report our conclusions about the
effectiveness of the disclosure controls and procedures based on our evaluation
as of the Evaluation Date;

5. The registrant's other certifying officer and I have disclosed, based on our
most recent evaluation, to the registrant's auditors and the audit committee of
registrant's board of directors (or persons performing the equivalent function):

     a) All significant deficiencies in the design or operation of internal
controls which could adversely affect the registrant's ability to record,
process, summarize and report financial data and have identified for the
registrant's auditors any material weaknesses in internal controls; and

     b) Any fraud, whether or not material, that involves management or other
employees who have a significant role in the registrant's internal controls; and


                                      -18-
<Page>

6. The registrant's other certifying officer and I have indicated in this
quarterly report whether or not there were significant changes in internal
controls or in other factors that could significantly affect internal controls
subsequent to the date of our most recent evaluation, including any corrective
actions with regard to significant deficiencies and material weaknesses.

Date: November 14, 2002

/s/ Paul Theodore Owens
-----------------------------
Paul Theodore Owens
Interim Chief Financial Officer


                                      -19-
<Page>

EXHIBIT INDEX

Exhibit No.     Description

10              Employment Agreement Between the Company and Ralph Sheridan
                dated July 11, 2002

99.1            Certification pursuant to Section 906 of the Sarbanes-Oxley Act
                of 2002.

99.2            Certification pursuant to Section 906 of the Sarbanes-Oxley Act
                of 2002.

                                      -20-