BROOKS AUTOMATION INC
10-Q, 1998-08-14
SPECIAL INDUSTRY MACHINERY, NEC
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<PAGE>
 
                                 UNITED STATES
                      SECURITIES AND EXCHANGE COMMISSION
                            Washington, D.C. 20549

                                   FORM 10-Q

(Mark One)
[X]  Quarterly Report Pursuant to Section 13 or 15(d) of the
       Securities Exchange Act of 1934
For the quarterly period ended: June 30, 1998

                                      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 0-25434
                              -------  ---------                        -------


                            BROOKS AUTOMATION, INC.
            (Exact name of registrant as specified in its charter)

           Delaware                                       04-3040660
           --------                                       ----------
(State or other jurisdiction of                        (I.R.S. Employer
 incorporation or organization)                       Identification No.)

                               15 Elizabeth Drive
                           Chelmsford, Massachusetts
                    (Address of principal executive offices)

                                     01824
                                   (Zip Code)

      Registrant's telephone number, including area code: (978) 262-2566

                 _____________________________________________

Indicate by check mark whether the registrant:  (1) has filed all reports
required to be filed by Section 13 or 15(d) of the Securities Exchange Act of
1934 during the preceding 12 months (or for such shorter period that the
registrant was required to file such reports), and (2) has been subject to such
filing requirements for the past 90 days.

                         Yes  X      NO    
                             ---        ---             
                                        
     As of August 10, 1998, there were outstanding 10,141,503 shares of the
     Company's Common Stock, $.01 par value.

     This report, including all exhibits and attachments, contains 19 pages.
                                                                   --        
<PAGE>
 
                            BROOKS AUTOMATION, INC.

                                     INDEX


                                        
                                                             PAGE
PART I    FINANCIAL INFORMATION                              NUMBER
- ------    ---------------------                              ------

Item 1     Financial Statements:
      
              Consolidated Balance Sheet                       3
      
              Consolidated Statement of Operations             4
       
              Consolidated Statement of Cash Flows             5
      
              Notes to Consolidated Financial
                 Statements                                  6-8

      
Item 2        Management's Discussion and Analysis of
                Financial Condition and Results 
                of Operations                               9-17
      
PART II   OTHER INFORMATION
- -------   ----------------- 
      
Item 6   Exhibits and Reports on Form 8-K                     18
 
Signatures                                                    19
 

                                 Page 2 of 19
<PAGE>
 
                            BROOKS AUTOMATION, INC.
                          CONSOLIDATED BALANCE SHEET
                   (IN THOUSANDS, EXCEPT SHARE RELATED DATA)



<TABLE> 
<CAPTION> 
                                                                       JUNE 30,      SEPTEMBER 30,
                                                                         1998             1997
                                                                     (UNAUDITED)
<S>                                                                  <C>             <C> 
ASSETS
Current assets:            
  Cash and cash equivalents                                           $  65,308       $  71,753        
  Accounts receivable, net of allowance for doubtful accounts
      of $486 and $160, respectively, and including related party
      receivables of $3,469 and $5,204, respectively                     23,560          28,408
  Inventories                                                            23,689          23,253
  Prepaid expenses and other current assets                               2,306           1,980
  Deferred income taxes                                                   4,963           1,710
                                                                      ---------       ---------
    Total current assets                                                119,826         127,104

Fixed assets, net                                                        18,315          19,054
Other assets                                                              3,687           3,572
                                                                      ---------       ---------
    Total assets                                                      $ 141,828       $ 149,730
                                                                      =========       =========


LIABILITIES AND STOCKHOLDERS' EQUITY
Current liabilities:
  Current portion of long-term debt and capital lease obligations     $      73       $     399
  Accounts payable                                                        5,843           9,125
  Accrued compensation and benefits                                       2,632           2,719
  Accrued expenses and other current liabilities                          2,465           2,193
                                                                      ---------       ---------
     Total current liabilities                                           11,013          14,436

Long-term debt and capital lease obligations                                 73             190
Deferred income taxes                                                       995             905
                                                                      ---------       ---------
     Total liabilities                                                   12,081          15,531
                                                                      ---------       ---------



Commitments and contingency                                                 -               -

Stockholders' equity:
  Preferred stock, $.01 par value; 1,000,000 shares authorized;
      none issued and outstanding                                           -               -
  Common stock, $.01 par value; 21,500,000 shares authorized;
      10,138,878 and 10,052,663 shares issued and outstanding,
      respectively                                                          101             101
  Additional paid-in capital                                            117,772         117,139
  Cumulative translation adjustment                                        (394)              5 
  Deferred compensation                                                    (320)           (416)
  Retained earnings                                                      12,588          17,370
                                                                      ---------       ---------
     Total stockholders' equity                                         129,747         134,199
                                                                      ---------       ---------
     Total liabilities and stockholders' equity                       $ 141,828       $ 149,730
                                                                      =========       =========
</TABLE> 


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

                                 Page 3 of 19
<PAGE>
 
                            BROOKS AUTOMATION, INC.
                     CONSOLIDATED STATEMENT OF OPERATIONS 
                     (IN THOUSANDS, EXCEPT PER SHARE DATA)
                                  (UNAUDITED)



<TABLE> 
<CAPTION> 
                                                      NINE MONTHS ENDED             THREE MONTHS ENDED
                                                           JUNE 30,                       JUNE 30,
                                                      1998         1997             1998          1997
<S>                                               <C>           <C>              <C>           <C> 
Revenues                                           $ 67,166     $ 55,603         $ 22,325      $ 23,059
Cost of revenues                                     52,665       38,094           17,105        15,428
                                                   --------     --------         --------      --------
    Gross profit                                     14,501       17,509            5,220         7,631
                                                   --------     --------         --------      --------
Operating expenses:
  Research and development                           13,140        9,722            3,407         3,614
  Selling, general and administrative                11,725        8,979            3,681         3,442
                                                   --------     --------         --------      --------
    Total operating expenses                         24,865       18,701            7,088         7,056
                                                   --------     --------         --------      --------
Income (loss) from operations                       (10,364)      (1,192)          (1,868)          575
Interest expense                                        178          415                4           158
Interest income                                       2,683           16              804           -
                                                   --------     --------         --------      --------
Income (loss) before income taxes                    (7,859)      (1,591)          (1,068)          417
Income tax provision (benefit)                       (3,077)        (354)            (316)          150
                                                   --------     --------         --------      --------
Net income (loss)                                  $ (4,782)    $ (1,237)        $   (752)     $    267
                                                   ========     ========         ========      ========


Basic income (loss) per share                      $  (0.47)    $  (0.16)        $  (0.07)     $   0.04
                                                   ========     ========         ========      ========

Diluted income (loss) per share                    $  (0.47)    $  (0.16)        $  (0.07)     $   0.03
                                                   ========     ========         ========      ========

Shares used in calculating basic income
    (loss) per share                                 10,091        7,614           10,114         7,606
                                                   ========     ========         ========      ========

Shares used in calculating diluted income
    (loss) per share                                 10,091        7,614           10,114         8,439
                                                   ========     ========         ========      ========
</TABLE> 


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

                                 Page 4 of 19
<PAGE>
 
                            BROOKS AUTOMATION, INC.
                     CONSOLIDATED STATEMENT OF CASH FLOWS 
                                (IN THOUSANDS)
                                  (UNAUDITED)



<TABLE> 
<CAPTION> 
                                                                           NINE MONTHS ENDED
                                                                                JUNE 30, 
                                                                           1998             1997
                                                                     
<S>                                                                    <C>             <C> 
INCREASE (DECREASE) IN CASH AND CASH EQUIVALENTS

CASH FLOWS FROM OPERATING ACTIVITIES
Net loss                                                                $  (4,782)      $  (1,237)
  Adjustments to reconcile net loss to net cash            
    provided by (used in) operating activities:
      Depreciation and amortization                                         4,221           3,290
      Compensation expense related to common stock options                     96              17
      Deferred income taxes                                                (2,930)            -
      Changes in operating assets and liabilities:            
        Accounts receivable                                                 4,714            (208)
        Inventories                                                          (285)         (3,315)
        Prepaid expenses and other current assets                            (355)         (1,949)
        Accounts payable                                                   (3,260)            803
        Accrued compensation and benefits                                     116            (507)
        Accrued expenses and other current liabilities                       (114)             75
                                                                        ---------       ---------
          Net cash used in operating activities                            (2,579)         (3,031)
                                                                        ---------       ---------


CASH FLOWS FROM INVESTING ACTIVITIES
Purchases of fixed assets                                                  (2,880)         (5,742)
Increase in other assets                                                     (510)         (1,740)
                                                                        ---------       ---------
          Net cash used in investing activities                            (3,390)         (7,482)


CASH FLOWS FROM FINANCING ACTIVITIES           
Net borrowings under line of credit                                           -             9,430
Principal payments on long-term debt and capital lease obligations           (444)           (315)
Proceeds from issuance of common stock                                        633             349
                                                                        ---------       ---------
          Net cash provided by financing activities                           189           9,464
                                                                        ---------       ---------


Effects of exchange rate changes on cash and cash equivalents                (665)             76
                                                                        ---------       ---------

Net decrease in cash and cash equivalents                                  (6,445)           (973)

Cash and cash equivalents, beginning of period                             71,753           2,102
                                                                        ---------       ---------

Cash and cash equivalents, end of period                                $  65,308       $   1,129
                                                                        =========       =========
</TABLE> 


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

                                 Page 5 of 19
<PAGE>
 
                            BROOKS AUTOMATION, INC.

                  NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
                                  (UNAUDITED)



1. BASIS OF  PRESENTATION
   ----------------------

   The accompanying unaudited consolidated financial statements of Brooks
   Automation, Inc. and its subsidiaries (the "Company") have been prepared in
   accordance with generally accepted accounting principles and with the
   instructions to Article 10 of Securities and Exchange Commission Regulation
   S-X.  Accordingly, they do not include all of the information and footnotes
   required by generally accepted accounting principles for complete financial
   statements.  In the opinion of management, all adjustments, consisting of
   normal recurring adjustments, considered necessary for a fair presentation
   have been included.  The accompanying unaudited consolidated financial
   statements should be read in conjunction with the audited consolidated
   financial statements of the Company which are included in the Company's
   Annual Report on Form 10-K for the year ended September 30, 1997.

   The results of operations for the nine months and three months ended June 30,
   1998 are not necessarily indicative of the results that may be expected for
   the fiscal year ending September 30, 1998.

2. INVENTORIES
   -----------
 
   <TABLE> 
   <CAPTION> 
   Inventories consist of the following:         June 30,   September 30,
   (in thousands)                                  1998         1997
                                                   ----         ---- 
   <S>                                           <C>        <C>   
   Raw materials and purchased parts              $16,819      $14,750
   Work-in-process                                  5,053        7,745
   Finished goods                                   1,817          758
                                                  -------      -------
                                                  $23,689      $23,253
                                                  =======      =======
</TABLE> 

3. EARNINGS (LOSSES) PER SHARE
   ---------------------------

   On October 1, 1997, the Company adopted Statement of Financial Accounting
   Standards No. 128, "Earnings per Share" (SFAS128), which establishes
   standards for computing and presenting earnings per share.  The new standard
   replaces the presentation of earnings per share as prescribed in Accounting
   Principles Board Opinion No. 15, "Earnings per Share" (APB15) with a
   presentation of basic and diluted earnings per share on the face of the
   statement of operations.  Basic earnings per share excludes dilution and is
   computed by dividing income available to common stockholders by the weighted-
   average number of common shares outstanding for the period.  The diluted
   earnings per share computation is similar to primary diluted earnings per
   share pursuant to APB15.  The Company has restated all prior period earnings
   per share amounts in accordance with the requirements of SFAS128. The
   dilutive potential shares have been excluded from the diluted earnings per
   share calculation for the three and nine month periods ended June 30, 1998
   and the nine month period ended June 30, 1997 due to their anti-dilutive
   effect.

                                 Page 6 of 19
<PAGE>
 
                            BROOKS AUTOMATION, INC.

                  NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
                                  (UNAUDITED)



   Below is a summary of the shares used in calculating basic and diluted
   earnings per share for the periods presented (in thousands):

<TABLE>
<CAPTION>
                                                Nine months ended  Three months ended
                                                     June 30,           June 30,
                                                  1998     1997      1998      1997
                                                  ----     ----      ----      ---- 
<S>                                             <C>       <C>      <C>        <C>

Weighted average shares outstanding             10,091    7,614     10,114     7,606
 
Dilutive potential common equivalent shares          0        0          0       833
                                                ------    -----     ------     -----
 
Weighted average common and dilutive
 potential common shares outstanding            10,091    7,614     10,114     8,439
                                                ======    =====     ======     =====
</TABLE>
                                        
4. RECENT ACCOUNTING PRONOUNCEMENTS
   --------------------------------

   In June 1997, the Financial Accounting Standards Board (FASB) issued
   Statement of Financial Accounting Standards No. 130, "Reporting Comprehensive
   Income" (SFAS 130) and Statement of Accounting Standards No. 131 "Disclosures
   about Segments of an Enterprise and Related Information" (SFAS 131).  SFAS
   130 establishes standards for reporting comprehensive income and its
   components in the consolidated financial statements.  SFAS 131 establishes
   standards for reporting information on operating segments in interim and
   annual financial statements.  The Company will adopt SFAS 130 and SFAS 131 on
   October 1, 1998.  Adoption of SFAS 130 and 131 will not have any effects on
   the Company's results of operations or financial position.

   In June 1998, the FASB issued Statement of Financial Accounting Standards No.
   133, "Accounting for Derivative Instruments and Hedging Activities" (SFAS
   133).  SFAS 133 is effective for all fiscal quarters of all fiscal years
   beginning after June 15, 1999 (October 1, 1999 for the Company).  SFAS 133
   requires that all derivative instruments be recorded on the balance sheet at
   their fair value.  Changes in the fair value of derivatives are recorded each
   period in current earnings or other comprehensive income, depending on
   whether a derivative is designated as part of a hedge transaction and, if it
   is, the type of hedge transaction.  Management of the Company anticipates
   that the adoption of SFAS 133 will not have a significant effect on the
   Company's results of operations or financial position.

5. SIGNIFICANT CUSTOMER AND RELATED PARTY INFORMATION
   --------------------------------------------------

   During the nine months ended June 30, 1998 and 1997, the Company had revenues
   from related parties representing 21% and 23% of revenues, respectively.
   During the three months ended June 30, 1998 and 1997, the Company had
   revenues from related parties representing 15% and 28% of revenues,
   respectively.  At June 30, 1998 and September 30, 1997, related party
   accounts receivable accounted for  18% of total accounts receivable.

   During the three months ended June 30, 1998, revenues from one customer (not
   a related party) represented 11% of revenues.  At June 30, 1998, accounts
   receivable from one customer accounted for 12% of accounts receivable. At
   September 30, 1997, accounts receivable from three customers accounted for
   46% of accounts receivable.

                                 Page 7 of 19
<PAGE>
 
                            BROOKS AUTOMATION, INC.

                  NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
                                  (UNAUDITED)



6. CONTINGENCY
   -----------

   There has been substantial litigation regarding patent and other intellectual
   property rights in the semiconductor related industries.  The Company has
   received notice from a third party alleging infringements of such party's
   patent rights, relating to cluster tool architecture, by certain of the
   Company's products.  In the event of litigation with respect to this claim,
   the Company is prepared to vigorously defend its position.  However, because
   patent litigation can be extremely expensive and time consuming, the Company
   may seek to obtain a license to one or more of the disputed patents.  Based
   upon currently available information, the Company would only do so if such
   license fees would not be material to the Company's consolidated financial
   statements.  Currently, the Company does not believe that it is probable that
   future events related to this threatened matter will have a material adverse
   effect on the Company's business.  The Company is currently unable to
   reasonably estimate any possible loss related to this matter.

                                 Page 8 of 19
<PAGE>
 
                            BROOKS AUTOMATION, INC.

               MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL
                      CONDITION AND RESULTS OF OPERATIONS



   Certain statements in this quarterly report constitute "forward-looking
   statements" which involve known risks, uncertainties and other factors which
   may cause the actual results, performance or achievements of the Company to
   be materially different from any future results, performance or achievements
   expressed or implied by such forward-looking statements.  Such factors
   include the factors that may affect future results set forth in Management's
   Discussion and Analysis of Financial Condition and Results of Operations
   which is included in this report.  Precautionary statements made herein
   should be read as being applicable to all related forward-looking statements
   wherever they appear in this report.


   OVERVIEW

   The predecessor of Brooks Automation, Inc. (the "Company") was organized in
   February 1989 and acquired the semiconductor wafer handling business of the
   Brooks Automation Division of Aeronca Electronics, Inc., a subsidiary of
   Fleet Aerospace Corporation, in March 1989.  The Company and its predecessors
   have been in the semiconductor wafer handling business since 1978.

   Since the acquisition in 1989, the Company has invested over $50.0 million in
   research and development focused primarily on vacuum transfer robots and
   other vacuum automation modules and systems.  In 1992, the Company introduced
   the family of vacuum central wafer handling systems and modules that forms
   the foundation of the Company's current business.  In 1994, the Company
   introduced a similar family of systems and modules for flat panel display
   substrates, including a next-generation magnetically driven vacuum transfer
   robot.  In 1996, the Company acquired Techware Systems Corporation (now
   Brooks Automation Software), a designer and supplier of integrated equipment
   control software for the semiconductor and related industries, expanding its
   software and control capability.  In 1997, the Company introduced a line of
   products for the atmospheric handling market, including in-line and
   controlled environment systems, robots, aligners and traversers.

   Many of the Company's customers purchase the Company's vacuum transfer robots
   and other modules before purchasing the Company's vacuum central wafer
   handling systems.  The Company believes that once a customer has selected the
   Company's products for a process tool, the customer is likely to rely on
   those products for the life of that process tool model, which can be in
   excess of five years.

   The Company records revenue from product sales upon shipment to the customer
   provided that no significant Company obligations remain and collection of the
   related receivable is deemed probable by management.  When insignificant
   Company obligations remain after shipment of the product, the Company accrues
   for the estimated cost of such obligations upon shipment.  Additionally, the
   Company accrues for any estimated warranty costs upon shipment.

   The majority of the Company's revenues have been generated by sales to
   customers in the United States, although the Company believes that a
   significant portion of these customers incorporate the Company's products
   into equipment sold to their foreign customers.  The Company's foreign sales
   have occurred principally in Japan, South Korea and Europe.

   The Company's foreign revenues are generally denominated in United States
   dollars.  Accordingly, foreign currency fluctuations have not had a
   significant impact on the comparison of the results of operations for the
   periods presented.  The costs and expenses of the Company's international
   subsidiaries are generally denominated in currencies other than the United
   States dollar.  However, since the functional currency of the Company's
   international subsidiaries is the local currency, foreign currency
   translation adjustments are reflected as a component of stockholders' equity.
   To

                                 Page 9 of 19
<PAGE>
 
   the extent that the Company expands its international operations or
   changes its pricing practices to denominate prices in foreign currencies, the
   Company will be exposed to increased risk of currency fluctuation.

   The Company's business is highly dependent upon the capital expenditures of
   semiconductor and flat panel display manufacturers which historically have
   been cyclical, and the Company's ability to develop, manufacture and sell new
   products and product enhancements.  The Company's results will also be
   affected, especially when measured on a quarterly basis, by the volume,
   composition and timing of orders, conditions in industries served by the
   Company, competition and general economic conditions.

   RESULTS OF OPERATIONS

   The following table sets forth certain financial data for the periods
   indicated as a percentage of revenues:

<TABLE>
<CAPTION>
                                                    Nine months ended   Three months ended
                                                         June 30,             June 30,
                                                      1998     1997       1998      1997
                                                      ----     ----       ----      ---- 
    <S>                                              <C>       <C>       <C>        <C>  

    Revenues                                         100.0%    100.0%    100.0%    100.0%
    Cost of revenues                                  78.4      68.5      76.6      66.9
                                                     -----     -----     -----     ----- 
    Gross profit                                      21.6      31.5      23.4      33.1 

    Operating expenses:
      Research and development                        19.6      17.5      15.3      15.7
      Selling, general and administrative             17.4      16.1      16.5      14.9
                                                     -----     -----     -----     -----
    Income (loss) from operations                    (15.4)     (2.1)     (8.4)      2.5
    Interest expense                                   0.3       0.8       0.0       0.7
    Interest income                                    4.0       0.0       3.6       0.0
                                                     -----     -----     -----     -----
    Income (loss) before income taxes                (11.7)     (2.9)     (4.8)      1.8
    Income tax provision (benefit)                    (4.6)     (0.7)     (1.4)      0.6
                                                     -----     -----     -----     -----
    Net income (loss)                                 (7.1)%    (2.2)%    (3.4)%     1.2%
                                                     =====     =====     =====     =====    
</TABLE> 

   
   THREE MONTHS AND NINE MONTHS ENDED JUNE 30,  1998 COMPARED WITH THREE MONTHS
   AND NINE MONTHS ENDED JUNE 30, 1997

   REVENUES
   Revenues for the three months ended June 30, 1998 decreased 3.2% to $22.3
   million compared with revenues of $23.1 million in the comparable prior
   fiscal period.  Revenues for the nine months ended June 30, 1998 increased
   20.8% to $67.2 million compared with revenues of $55.6 million in the
   comparable prior fiscal period. Revenues from 200mm vacuum central wafer
   handling systems and components decreased 5.8% or $900,000 for the three
   months ended June 30, 1998 compared to the comparable prior fiscal period,
   and increased 31.3% or $9.7 million for the nine months ended June 30, 1998
   compared to the comparable prior fiscal period.  The decrease in 200mm
   product revenues combined with decreases in service and control software
   revenues in the current quarter compared to the quarter ended June 30, 1997
   were partially offset by an increase in 300mm product revenues.  Increased
   revenues from shipments of 200mm and 300mm products as well as increased
   service revenues, partially offset by decreased flat panel display product
   revenues, contributed to the overall increase in revenues in the first nine
   months of fiscal 1998 compared to the nine months ended June 30, 1997.  The
   Company expects revenues in the fiscal 1998 fourth quarter

                                       Page 10 of 19
<PAGE>

                            BROOKS AUTOMATION, INC.

               MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL
                      CONDITION AND RESULTS OF OPERATIONS


 
   will decrease at least 15% compared with the three months ended June 30, 1998
   due primarily to the prolonged economic downturn currently impacting the
   semiconductor industry and related fabrication equipment sector.

   Foreign revenues for the three months ended June 30, 1998 increased 73.1% to
   $11.2 million (50.2% of revenues), including $10.7 million of direct sales to
   Asian customers, compared with foreign revenues of $6.5 million (28.0% of
   revenues), including $4.6 million of direct sales to Asian customers in the
   comparable prior fiscal period.  Foreign revenues for the nine months ended
   June 30, 1998 increased 47.7% to $25.3 million (37.6% of revenues), including
   $21.3 million of direct sales to Asian customers, compared with foreign
   revenues of $17.1 million (30.8% of revenues), including $13.0 million of
   direct sales to Asian customers in the comparable prior fiscal period.  The
   Company expects that foreign revenues will continue to account for a
   significant portion of total revenues in fiscal 1998.  However, there can be
   no assurance that the geographical growth rates, if any, in the foreseeable
   future, particularly in Asia which is suffering regional economic downturns,
   will be comparable to those achieved in the first nine months of fiscal 1998.

   GROSS PROFIT
   Gross profit as a percentage of revenues decreased to 23.4% and 21.6%,
   respectively, for the three months and nine months ended June 30, 1998
   compared with 33.1% and 31.5%, respectively, for the comparable prior fiscal
   periods. The decrease in the gross profit percentage for the three months
   ended June 30, 1998 is attributable primarily to decreased revenues from
   product categories with higher gross profit contribution margins, primarily
   service and control software, as well as volume related underabsorption of
   fixed manufacturing overhead.  The decrease in the gross profit percentage
   for the nine months ended June 30, 1998 is attributable to $4.2 million of
   nonrecurring charges in the second quarter of fiscal 1998 related to
   inventory reserves and severance costs, underutilization of manufacturing
   capacity (due in part to customer requested shipment delays primarily in the
   first half of fiscal 1998) and pricing pressure from volume production
   customers.

   Global support costs, including primarily personnel costs and travel
   expenses, decreased 23.1% to $1.4 million (6.2% of revenues) for the three
   months ended June 30, 1998 from $1.8 million (7.8% of revenues) in the
   comparable prior fiscal period.  Global support costs decreased 4.6% to $4.5
   million (6.7% of revenues) for the nine months ended June 30, 1998 from $4.7
   million (8.5% of revenues) in the comparable prior fiscal period.  The
   overall decrease in global support costs reflects the impact of increased
   global cost efficiencies and overall cost controlling measures.

   RESEARCH AND DEVELOPMENT
   Research and development expenses decreased 5.7% to $3.4 million (15.3% of
   revenues) for the three months ended June 30, 1998 from $3.6 million (15.7%
   of revenues) in the comparable prior fiscal period. Research and development
   expenses increased 35.2% to $13.1 million (19.6% of revenues) for the nine
   months ended June 30, 1998 from $9.7 million (17.5% of revenues) in the
   comparable prior fiscal period.  The decrease in research and development
   expenses in the current quarter is due primarily to lower personnel costs
   following a reduction in headcount in the second quarter of fiscal 1998.  The
   increase in research and development expenses in the nine months ended June
   30, 1998 primarily resulted from incremental spending associated with the
   launch of new atmospheric products and the transition to next generation
   vacuum wafer handling products.

   SELLING, GENERAL AND ADMINISTRATIVE
   Selling, general and administrative expenses increased 6.9% to $3.7 million
   (16.5% of revenues) for the three months ended June 30, 1998 from $3.4
   million (14.9% of revenues) in the comparable prior fiscal period. Selling,
   general and administrative expenses increased 30.6% to $11.7 million (17.4%
   of revenues) for the nine months ended June 30, 1998 from $9.0 million (16.1%
   of revenues) in the comparable prior fiscal period.  The increase in selling,
   general

                                 Page 11 of 19
<PAGE>

                            BROOKS AUTOMATION, INC.

               MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL
                      CONDITION AND RESULTS OF OPERATIONS

   and administrative expenses is due primarily to the worldwide expansion of
   the Company's sales and administrative organizations.


   INTEREST EXPENSE AND INTEREST INCOME
   Interest expense for the three months ended June 30, 1998 decreased to $4,000
   (0.0% of revenues) from $158,000 (0.8% of revenues) in the comparable prior
   fiscal period.  Interest expense for the nine months ended June 30, 1998
   decreased to $178,000 (0.3% of revenues) from $415,000 (0.8% of revenues) in
   the comparable prior fiscal period.  The decrease in interest expense is due
   primarily to the repayment of short-term borrowings under revolving credit
   facilities in September 1997, partially offset by amortization of $115,000 of
   deferred financing costs in the first quarter of fiscal year 1998.  There
   were no borrowings outstanding under the revolving credit facilities at June
   30, 1998.  The amortization of deferred financing costs included in interest
   expense in the first quarter of fiscal 1998 resulted from the repayment of
   the related note payable.  Interest income increased to $804,000 (3.6% of
   revenues) for the three months ended June 30, 1998.  Interest income for the
   nine months ended June 30, 1998 increased to $2.7 million (4.0% of revenues)
   from $16,000 in the comparable prior fiscal period. The increases in interest
   income are due to higher cash and investment balances during the first nine
   months of fiscal 1998, resulting from the Company's $80.8 million public
   stock offering in September 1997.

   INCOME TAX PROVISION (BENEFIT)
   The Company recorded net tax benefits of $316,000 and $3.1 million,
   respectively, during the three months and nine months ended June 30, 1998,
   primarily due to the anticipated future tax benefit of domestic net operating
   losses and research and development tax credit carryforwards generated during
   1998.


   LIQUIDITY AND CAPITAL RESOURCES

   As of June 30, 1998, the Company had working capital of $108.8 million,
   including $65.3 million of cash and cash equivalents, compared with working
   capital of $112.7 million, including $71.8 million of cash and cash
   equivalents, as of September 30, 1997. During the nine months ended June 30,
   1998, the Company used net cash of $2.6 million in operating activities,
   which was primarily the result of the net loss for the period combined with
   an increase in the deferred tax asset attributable to net operating losses
   generated during the period and the repayment of current liabilities. The
   overall decrease in cash due to the aforementioned activities was partially
   offset by a decrease of $4.7 million in the accounts receivable balance.
   Investing activities during the nine months ended June 30, 1998 consisted
   primarily of capital spending for information systems and facility
   improvements. The Company anticipates that it will continue to make capital
   expenditures to support its business activities. Financing activities during
   the nine months ended June 30, 1998 consisted primarily of the issuance of
   common stock under the Company's employee stock purchase plan and the
   repayment of long-term debt and capital lease obligations. As of June 30,
   1998, the Company elected to terminate its credit facilities. There were no
   borrowings outstanding at June 30, 1998. The Company believes that available
   funds will be adequate to fund the Company's currently planned working
   capital and capital expenditure requirements for the next twelve months.

   The Company has received notice from a third-party alleging infringements of
   such party's patent rights by certain of the Company's products. The Company
   believes the patents claimed may be invalid. In the event of litigation with
   respect to this claim, the Company is prepared to vigorously defend its
   position. Currently, the Company does not believe that it is probable that
   future events related to this threatened matter will have a material adverse
   effect on the Company's business; however, there can be no assurance that
   this will be the case. The Company is currently unable to reasonably estimate
   any possible loss related to this matter.

   

                                 Page 12 of 19
<PAGE>

                            BROOKS AUTOMATION, INC.

               MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL
                      CONDITION AND RESULTS OF OPERATIONS

 
   FACTORS THAT MAY AFFECT FUTURE RESULTS

   QUARTERLY FLUCTUATIONS IN OPERATING RESULTS AND MARKET PRICE OF SECURITIES
   The Company's operating results have in the past fluctuated and may in the
   future continue to fluctuate significantly depending upon a variety of
   factors. Such factors may include: the demand for semiconductors in general;
   cyclicality in the market for semiconductor manufacturing equipment; the
   timing and size of orders from the Company's customer base; the ability of
   the Company to manufacture, test and deliver products in a timely and cost
   effective manner; the ability of the Company's competitors to obtain orders
   from the Company's customers; the timing of new product announcements and
   releases by the Company and its competitors; the mix of products sold by the
   Company; and competitive pricing pressures.

   The Company has historically derived a substantial portion of its quarterly
   and annual revenues from the sale of a relatively small number of
   semiconductor and flat panel display substrate handling systems, which have
   relatively high selling prices compared to its other products. As a result,
   the precise timing of the recognition of revenue from an order for one or a
   small number of systems can have a significant impact on the Company's total
   revenues and operating results for a particular period. The Company's
   operating results for a particular period could be adversely affected if
   orders for a small number of systems are canceled or rescheduled by customers
   or cannot be filled in time to recognize revenue during that period due to,
   for example, unanticipated manufacturing, testing, shipping or product
   acceptance delays. The Company's expense levels are based, in large part, on
   the Company's expectations as to future revenues and are, therefore,
   relatively fixed in the short term. If revenue levels fall below
   expectations, net income will be disproportionately and adversely affected.
   The impact of these and other factors on the Company's revenues and operating
   results in any future period cannot be forecast with any degree of certainty.
   These factors could have a material adverse effect on the Company's business,
   future financial condition, revenues and results of operations.

   DEPENDENCE ON SEMICONDUCTOR INDUSTRY
   The Company's business is significantly dependent on capital expenditures by
   manufacturers of semiconductors. The semiconductor industry is highly
   cyclical and is presently experiencing a period of oversupply, resulting in
   significantly reduced demand for capital equipment, including the products
   manufactured and marketed by the Company. The Company's financial condition,
   revenues and results of operations have been materially and adversely
   affected by semiconductor industry downturns and may be materially
   adversely affected by future downturns. The Company believes that downturns
   in the semiconductor manufacturing industry will occur in the future, and
   will result in decreased demand for semiconductor manufacturing equipment. In
   addition, the Company believes (on the basis of its experience during the
   course of the present downturn) that its ability to reduce expenses in a
   future downturn will be constrained by the need for continual investment in
   research and development, and the need to maintain ongoing customer service
   and support capability. Accordingly, any downturn in the semiconductor
   industry could have a material adverse effect on the Company's business,
   future financial condition and results of operations.

   CUSTOMER CONCENTRATION
   Relatively few customers account for a substantial portion of the Company's
   revenues. Sales to the Company's ten largest customers in the nine months
   ended June 30, 1998, fiscal 1997 and fiscal 1996 accounted for 72%, 71% and
   69% of revenues, respectively.  In the nine months ended June 30, 1998 and in
   fiscal 1997 and fiscal 1996, sales to Lam Research Corporation ("Lam"), the
   Company's largest customer in these periods, accounted for 20%, 21% and 21%
   of the Company's revenues, respectively. The Company expects that sales to
   Lam will continue to represent a significant portion of the Company's
   revenues for the foreseeable future. The Company's customers, including Lam,
   generally do not enter into long-term agreements obligating them to purchase
   the Company's products. A reduction or delay in orders from Lam or other
   significant customers, including reductions or delays due to market, economic
   or

                                 Page 13 of 19
<PAGE>
 
                            BROOKS AUTOMATION, INC.

               MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL
                      CONDITION AND RESULTS OF OPERATIONS

 
   competitive conditions in the semiconductor or flat panel display industries,
   could have a material adverse effect on the Company's business, financial
   condition and results of operations.

   RELIANCE ON OEM CUSTOMERS; LENGTHY SALES CYCLE
   The Company's products are principally sold to OEMs which incorporate the
   Company's products into their equipment. Due to the significant capital
   commitments usually incurred by semiconductor and flat panel display
   manufacturers in their purchases of these OEMs' equipment, these
   manufacturers demand highly reliable products which may require several years
   for OEMs to develop. The Company's revenues are therefore primarily dependent
   upon the timing and effectiveness of the efforts of its OEM customers in
   developing and marketing equipment incorporating the Company's products.

   The Company's new products are generally incorporated into an OEM customer's
   process tools at the design stage. However, customer decisions to use the
   Company's products, which can often require significant expenditures by the
   Company without any assurance of success, often precede the generation of
   volume sales, if any, by a year or more. There can be no assurance that the
   Company will continue to achieve design wins, that the process tools
   manufactured by the Company's customers will be introduced in a timely manner
   or that such systems will achieve market acceptance. The Company's or its
   customers' failure to develop and introduce new products successfully and in
   a timely manner could materially and adversely affect the Company's business,
   financial condition and results of operations.

   RISKS OF INTERNATIONAL SALES AND OPERATIONS
   During the nine months ended June 30, 1998 and in fiscal 1997 and fiscal
   1996, the Company derived 38%, 38% and 20% of its revenues from customers
   located outside the United States.  The Company anticipates that
   international revenues will continue to account for a significant portion of
   its revenues.  To support its international customers, the Company maintains
   subsidiaries in Japan, Europe, South Korea, Taiwan and Singapore.  There can
   be no assurance that the Company will be able to manage these operations
   effectively or that the Company's investment in these activities will enable
   it to compete successfully in international markets or to meet the service
   and support needs of its customers.

   The Company will continue to be affected, for the foreseeable future, by
   unstable Asian economies, particularly in Japan and South Korea.  As a
   result, there are uncertainties that may affect future operations.  It is not
   possible to determine the future effect a continuation of the Asian economic
   crisis may have on the Company's liquidity and earnings.

   Additionally, a significant portion of the Company's revenues and operations
   could be subject to certain risks, including tariffs, foreign government
   standards and regulations and other barriers, difficulties in staffing and
   managing foreign subsidiary operations, currency exchange risks and exchange
   controls, adverse tax consequences and difficulty in accounts receivable
   collection. International trade regulations, such as United States export
   controls, could change in the future and make it more difficult for the
   Company to export its products to various countries. There can be no
   assurance that any of these factors will not have a material adverse effect
   on the Company's business, financial condition and results of operations.

   HIGHLY COMPETITIVE INDUSTRY
   The markets for the Company's products are highly competitive and subject to
   rapid technological change. The Company believes that its primary competition
   is from integrated OEMs that satisfy their semiconductor and flat panel
   display handling needs in-house rather than by purchasing systems or modules
   from an independent supplier such as the Company. Many of these other
   potential competitors have substantially greater resources than the Company.
   There

                                 Page 14 of 19
<PAGE>
                            BROOKS AUTOMATION, INC.

               MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL
                      CONDITION AND RESULTS OF OPERATIONS

 
   can be no assurance that the Company will be successful in selling its
   products to OEMs that currently satisfy their substrate handling needs in-
   house, regardless of the performance or the price of the Company's products.
   Moreover, there can be no assurance that integrated OEMs will not begin to
   commercialize their handling capabilities. Competitors may develop superior
   products or products of similar quality at the same or lower prices. Other
   technical innovations may impair the Company's ability to market its
   products. There can be no assurance that the Company will be able to compete
   successfully.

   NEW PRODUCTS AND RAPID TECHNOLOGICAL CHANGE
   The semiconductor and flat panel display manufacturing industries have been
   characterized by rapid technological change and evolving industry
   requirements and standards. The Company believes that these trends will
   continue. The Company's success will depend upon its ability to enhance its
   existing products and to develop and market new products to meet customer
   requirements. Successful product development and introduction depends on a
   number of factors, including accurate new product definition, timely
   completion and introduction of new product designs and market acceptance of
   the Company's products and its customers' products. Currently, the Company's
   major development programs include expanding its product offerings of
   semiconductor substrate handling systems to address emerging industry
   requirements for 300mm wafer and fourth generation flat panel substrates, as
   well as wafer handling systems and modules for atmospheric process tools. In
   addition, the Company continues to develop and enhance its process control
   software product offerings. There can be no assurance that the Company will
   adjust to changing market conditions or be successful in introducing products
   or product enhancements on a timely basis, if at all, or that the Company
   will be able to market successfully these products and product enhancements
   once developed. Further, there can be no assurance that the Company's
   products will not be rendered obsolete by new industry standards or changing
   technology.

   ATTRACTION AND RETENTION OF KEY PERSONNEL
   Due to the level of technical and marketing expertise necessary to support
   its existing and new customers, the Company must attract and retain highly
   qualified and well-trained domestic and international personnel. There is a
   limited number of persons with the requisite skills to serve in these
   positions and it may become increasingly difficult for the Company to hire
   such personnel.  Competition for such personnel is intense and there can be
   no assurance that the Company will attract and retain personnel necessary for
   the development of its business.

   RISKS ASSOCIATED WITH POSSIBLE ACQUISITIONS
   From time to time, the Company pursues potential acquisitions of businesses,
   products and technologies that could complement or expand the Company's
   business. The Company currently has no commitments or agreements with respect
   to any material acquisitions.  There can be no assurance that the Company
   will be able to successfully negotiate the terms of any such acquisition,
   finance such acquisition or integrate such acquired businesses, products or
   technologies into the Company's existing business and products. The
   negotiation of potential acquisitions as well as the integration of an
   acquired business could cause diversion of management's time and resources.
   Acquisitions by the Company could result in potentially dilutive issuances of
   equity securities, the incurrence of debt and contingent liabilities and
   amortization expenses. If any such acquisition were to occur, there can be no
   assurance that, whether or not consummated, any such acquisition would not
   have a material adverse effect on the Company's business, future financial
   condition and results of operations.

   INTELLECTUAL PROPERTY PROTECTION AND RELATED CONTINGENCY
   There can be no assurance that the Company's pending patent applications or
   any future applications will be approved, that any patents will provide it
   with competitive advantages or will not be challenged by third parties, or
   that the patents of others will not have an adverse effect on the Company's
   ability to do business. Because foreign patents may afford less protection
   under foreign law than is available under United States patent law, there can
   be no assurance

                                 Page 15 of 19
<PAGE>
 
                            BROOKS AUTOMATION, INC.

               MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL
                      CONDITION AND RESULTS OF OPERATIONS

 
   that any such patents issued to the Company will adequately protect the
   Company's proprietary information. There can be no assurance that others will
   not independently develop similar products, duplicate the Company's products
   or, if patents are issued to the Company, design around the patents issued to
   the Company.

   Others may have filed and in the future may file patent applications that are
   similar or identical to those of the Company. To determine the priority of
   inventions, the Company may have to participate in interference proceedings
   declared by the United States Patent and Trademark Office that could result
   in substantial cost to the Company. No assurance can be given that any such
   patent application will not have priority over patent applications filed by
   the Company.

   The Company also relies upon trade secret protection, employee and third-
   party nondisclosure agreements and other intellectual property protection
   methods to protect its confidential and proprietary information. Despite
   these efforts, there can be no assurance that others will not independently
   develop substantially equivalent proprietary information and techniques or
   otherwise gain access to the Company's trade secrets or disclose such
   technology or that the Company can meaningfully protect its trade secrets.

   There has been substantial litigation regarding patent and other intellectual
   property rights in the semiconductor related industries.  The Company had
   received notice from General Signal Corporation ("General Signal") alleging
   infringements of General Signal's patent rights, relating to cluster tool
   architecture, by certain of the Company's products.  The notification advised
   the Company that General Signal was attempting to enforce its rights to those
   patents in litigation against Applied Materials, Inc. ("Applied Materials"),
   and that, at the conclusion of that litigation, General Signal intended to
   enforce its rights against the Company and others.  According to a press
   release issued by Applied Materials, Applied Materials settled its litigation
   with General Signal by acquiring ownership of five General Signal patents.
   Although not verified, these five patents would appear to be the patents
   referred to by General Signal in its prior notice to the Company.  Applied
   Materials has not contacted the Company regarding these patents.

   In 1992, at the time that General Signal first raised patent claims in the
   cluster tool area, the Company joined with six major semiconductor process
   tool equipment manufacturers in forming an "Ad Hoc Committee for the Defense
   against General Signal Cluster Tool Patents."  At that time, the members of
   the Ad Hoc Committee notified General Signal that the member companies were
   of the opinion that the General Signal patents were invalid based on (i)
   prior art, (ii) inequitable conduct before the Patent & Trademark Office and
   (iii) estoppel as a result of General Signal's activities in establishing
   standards for cluster tools and interfaces within the semiconductor industry.
   The Company believes that the position taken by the Ad Hoc Committee remains
   valid.  However, if the holder of these patents were to seek to enforce these
   patents against the Company, there can be no assurance that the Company would
   prevail in such litigation.

   The Company has in the past been, and may in the future be, notified that it
   may be infringing intellectual property rights possessed by other third
   parties. Any patent litigation would be costly and could divert the efforts
   and attention of the Company's management and technical personnel, which
   could have a material adverse effect on the Company's business, financial
   condition and results of operations. There can be no assurance that
   infringement claims by third parties or other claims for indemnification by
   customers or end users of the Company's products resulting from infringement
   claims will not be asserted in the future or that such assertions, if proven
   to be true, will not materially and adversely affect the Company's business,
   financial condition and results of operations. If any such claims are
   asserted against the Company's intellectual property rights it may seek to
   enter into a royalty or licensing arrangement. There can be no assurance,
   however, that a license will be available on reasonable terms or at all. The
   Company could decide, in the alternative to resort to litigation to challenge
   such claims or to design around the 

                                 Page 16 of 19
<PAGE>

                            BROOKS AUTOMATION, INC.

               MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL
                      CONDITION AND RESULTS OF OPERATIONS

 
   patented technology. Such actions could be costly and would divert the
   efforts and attention of the Company's management and technical personnel,
   which could materially and adversely affect the Company's business, financial
   condition and results of operations.

   YEAR 2000 CONSIDERATIONS
   The Company has established a project to perform an analysis of its products
   and services and undertake any work necessary to ensure that they continue to
   operate correctly into the year 2000.  The costs associated with this project
   will be expensed as incurred.  At this time, the Company is unable to
   determine whether such costs will be material to its financial position or
   results of operations.

   VOLATILITY OF STOCK PRICE
   The Company believes that a variety of factors could cause the price of the
   Company's Common Stock to fluctuate, perhaps substantially, including:
   announcements of developments related to the Company's business; quarterly
   fluctuations in the Company's actual or anticipated operating results and
   order levels; general conditions in the semiconductor and flat panel display
   industries or the worldwide economy; announcements of technological
   innovations; new products or product enhancements by the Company or its
   competitors; developments in patents or other intellectual property rights
   and litigation; and developments in the Company's relationships with its
   customers and suppliers. In addition, in recent years the stock market in
   general and the market for shares of small capitalization and semiconductor
   industry-related companies in particular, have experienced extreme price
   fluctuations which have often been unrelated to the operating performance of
   affected companies. Any such fluctuations in the future could adversely
   affect the market price of the Company's Common Stock. There can be no
   assurance that the market price of the Common Stock of the Company will not
   decline.

                                 Page 17 of 19
<PAGE>
 
                            BROOKS AUTOMATION, INC.

                          PART II: OTHER INFORMATION






Item 6 (a)    EXHIBITS.
              ---------

              Exhibit No. 
              ----------- 
              27.01              Financial Data Schedule


Item 6 (b)    REPORTS ON FORM 8-K.
              --------------------

              No reports on Form 8-K were filed during the quarter ended
              June 30, 1998.

                                 Page 18 of 19
<PAGE>
 
                                  SIGNATURES


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



                            BROOKS AUTOMATION, INC.
                                        
                                        


                                        
August 14,1998                     /s/ Robert J. Therrien
- --------------                     ---------------------------------------------
[Date]                             Robert J. Therrien
                                   Chief Executive Officer,
                                   President and Treasurer

August 14, 1998                    /s/ Deborah D. Fox
- ---------------                    -----------------------------------------
[Date]                             Deborah D. Fox
                                   Corporate Controller and
                                   Chief Accounting Officer

                                 Page 19 of 19

<TABLE> <S> <C>

<PAGE>
 
<ARTICLE> 5
<LEGEND>
THIS SCHEDULE CONTAINS SUMMARY FINANCIAL INFORMATION EXTRACTED FROM FORM 10-Q
AND IS QUALIFIED IN ITS ENTIRETY BY REFERENCE TO SUCH FINANCIAL STATEMENTS.
</LEGEND>
<MULTIPLIER> 1,000
       
<S>                             <C>
<PERIOD-TYPE>                   9-MOS
<FISCAL-YEAR-END>                          SEP-30-1998
<PERIOD-START>                             OCT-01-1997
<PERIOD-END>                               JUN-30-1998
<CASH>                                          65,308
<SECURITIES>                                         0
<RECEIVABLES>                                   23,560
<ALLOWANCES>                                     (486)
<INVENTORY>                                     23,689
<CURRENT-ASSETS>                               119,826
<PP&E>                                          31,676
<DEPRECIATION>                                (13,361)
<TOTAL-ASSETS>                                 141,828
<CURRENT-LIABILITIES>                           11,013
<BONDS>                                              0
                                0
                                          0
<COMMON>                                           101
<OTHER-SE>                                     129,646
<TOTAL-LIABILITY-AND-EQUITY>                   141,828
<SALES>                                         67,166
<TOTAL-REVENUES>                                67,166
<CGS>                                           52,665
<TOTAL-COSTS>                                   24,865
<OTHER-EXPENSES>                                     0
<LOSS-PROVISION>                                     0
<INTEREST-EXPENSE>                                 178
<INCOME-PRETAX>                                (7,859)
<INCOME-TAX>                                   (3,077)
<INCOME-CONTINUING>                            (4,782)
<DISCONTINUED>                                       0
<EXTRAORDINARY>                                      0
<CHANGES>                                            0
<NET-INCOME>                                   (4,782)
<EPS-PRIMARY>                                   (0.47)
<EPS-DILUTED>                                   (0.47)
        

</TABLE>


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