BROOKS AUTOMATION INC
10-Q, 1999-02-16
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:   December 31, 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 February 9, 1999, there were outstanding 11,046,250 shares of
          the Company's Common Stock, $0.01 par value.

          This report, including all exhibits and attachments, contains 20
          pages.
<PAGE>
 
                            BROOKS AUTOMATION, INC.

                                     INDEX


<TABLE>
<CAPTION>
<S>           <C>                                                                     <C>   
                                                                                          Page
PART I.        FINANCIAL INFORMATION                                                     Number
- -------        ---------------------                                                     ------
Item 1          Financial Statements:

                Condensed Consolidated Balance Sheet at December 31, 1998,
                and September 30, 1998                                                        3
 
                Condensed  Consolidated Statement of Operations for the three months
                ended December 31, 1998 and 1997                                              4
 
                Condensed Consolidated Statement of Cash Flows for the three months
                ended December 31, 1998 and 1997                                              5
 
                Notes to Condensed Consolidated Financial Statements                         6-7
 
Item 2          Management's Discussion and Analysis of Financial Condition and Results
                of Operations                                                                8-11

Item 3          Quantitative and Qualitative Disclosures about Market Risk                   12
 
Risk Factors                                                                                 13-16
 
PART II.        OTHER INFORMATION
- --------        ----------------- 
 
Item 6          Exhibits and Reports on Form 8-K                                             17
 
Signatures                                                                                   18
</TABLE>

                                 Page 2 of 18

<PAGE>
 
<TABLE>
<CAPTION>
                            BROOKS AUTOMATION, INC.
                     CONDENSED CONSOLIDATED BALANCE SHEET
 
 
(In thousands, except share data)                                            
                                             December 31,     September 30,  
                                                 1998              1998      
                                            ---------------  --------------- 
                                              (unaudited)                    
<S>                                         <C>               <C>     
Assets                                                                       
Current assets:                                                              
 Cash and cash equivalents                        $ 70,411         $ 68,161  
 Accounts receivable, net of                                                 
    allowance for doubtful accounts                                          
    of $1,898 and including related                                          
    party receivables of $906 and 
    $2,365, respectively                            18,660           20,701  
 Inventories                                        17,237           19,589  
 Prepaid expenses and other                                                  
    current assets                                   1,866            3,535  
 Deferred income taxes                               6,204            6,106  
                                                  --------         --------  
    Total current assets                           114,378          118,092  
                                                                             
Fixed assets, net                                   18,255           18,606  
Other assets                                         4,532            4,254  
                                                  --------         --------  
    Total assets                                  $137,165         $140,952  
                                                  ========         ========  
                                                                             
Liabilities and stockholders' equity                                         
                                                                             
Current liabilities:                                                         
 Accounts payable                                 $  2,938         $  5,505  
 Deferred revenue                                    3,086            2,935  
 Accrued expenses and other                                                  
    current liabilities                              9,052            9,731  
                                                  --------         --------  
    Total current liabilities                       15,076           18,171  
                                                                             
Long-term debt and capital                                                   
    lease obligations                                   35              130  
Deferred income taxes                                  738              888  
                                                  --------         --------  
    Total liabilities                               15,849           19,189  
                                                  --------         --------  
                                                                             
Stockholders' equity:                                                        
 Preferred stock, $0.01 par                                                  
    value; 1,000,000 shares                                                  
    authorized;  none issued                                                 
    and outstanding                                      -                -  
 Common stock, $0.01 par value;                                              
    21,500,000 shares authorized;                                            
    11,019,270 and 11,007,281                                                
    shares issued and outstanding,                                           
    respectively                                       110              110  
 Additional paid-in capital                        128,884          128,839  
 Cumulative translation adjustment                    (461)            (536) 
 Deferred compensation                                (111)            (119) 
 Accumulated deficit                                (7,106)          (6,531) 
                                                  --------         --------  
    Total stockholders' equity                     121,316          121,763  
                                                  --------         --------  
    Total liabilities and                                                    
    stockholders' equity                          $137,165         $140,952 
                                                  ========         ========  
</TABLE>
                                                                             
 The accompanying notes are an integral part of these condensed consolidated
 financial statements.

                                 Page 3 of 18
<PAGE>
 
                            BROOKS AUTOMATION, INC.
                CONDENSED CONSOLIDATED STATEMENT OF OPERATIONS
                                  (unaudited)

(In thousands, except share data)

<TABLE>
<CAPTION>
                                        Three months ended December 31,
                                              1998           1997
                                           ----------    ----------
<S>                                       <C>             <C> 
Revenues:                                          
 Product, including related                        
   party revenues of $705                          
   and $4,745, respectively                   $15,155       $25,033
 Services                                       4,654         4,615
                                              -------       -------
   Total revenues                              19,809        29,648
                                              -------       -------
                                             
Cost of revenues:                            
 Product                                        8,568        15,038
 Services                                       2,500         2,971
                                              -------       -------
   Total cost of revenues                      11,068        18,009
                                              -------       -------
                                             
Gross profit                                    8,741        11,639
                                              -------       -------
Operating expenses:                          
 Research and development                       4,092         6,744
 Selling, general and
   administrative                               5,727         7,075
                                              -------       -------
   Total operating expenses                     9,819        13,819
                                              -------       -------
                                             
Loss from operations                           (1,078)       (2,180)
Interest income                                   757           955
Interest expense                                   33           265
                                              -------       -------
                                             
Loss before income taxes                         (354)       (1,490)
Income tax provision                              221         1,364
                                              -------       -------
                                             
Net loss                                         (575)       (2,854)
Dividends on preferred                        
 stock                                              -          (131)
                                              -------       -------  
                                             
Net loss attributable to                      
 common stockholders                          $  (575)      $(2,985) 
                                              =======       =======  
                                             
Loss per share:                              
 Basic                                        $ (0.05)      $ (0.29)
 Diluted                                      $ (0.05)      $ (0.29)
                                             
Shares used in computing loss 
   per share:                                
 Basic                                         11,010        10,194
 Diluted                                       11,010        10,194
 
</TABLE>

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

                                 Page 4 of 18
<PAGE>
 
                            BROOKS AUTOMATION, INC.
                 CONDENSED CONSOLIDATED STATEMENT OF CASH FLOWS
                                  (unaudited)
<TABLE>
<CAPTION>
 
 
                                                                                   Three months ended December 31,
(In thousands)                                                                        1998                 1997
                                                                                   -----------          ----------  
<S>                                                                               <C>                  <C> 
Cash flows from operating activities                                             
Net loss                                                                           $      (575)         $   (2,854)
 Adjustments to reconcile net loss to net cash provided by                       
  operating activities:                                                                   
   Depreciation and amortization                                                         1,686               2,024 
   Compensation expense related to common stock options                                      8                  26 
   Deferred income taxes                                                                  (330)              1,334 
   Changes in operating assets and liabilities:                                                 
     Accounts receivable                                                                 2,078               4,647
     Inventories                                                                         2,376              (2,940)
     Prepaid expenses and other current assets                                           1,703                (347) 
     Accounts payable                                                                   (2,568)                262 
     Deferred revenue                                                                      174                (178)
     Accrued expenses and other current liabilities                                       (851)               (718)
                                                                                   -----------          ----------  
        Net cash provided by operating activities                                        3,701               1,256
                                                                                   -----------          ----------  

Cash flows from investing activities                                                 
Purchases of fixed assets                                                               (1,292)             (1,624)
Increase in other assets                                                                  (235)               (413)
                                                                                   -----------          ----------  
        Net cash used in investing activities                                           (1,527)             (2,037) 
                                                                                   -----------          ----------  
                                                                                     
Cash flows from financing activities                                                                            
Payments on long-term debt                                                                (102)               (322)
Proceeds from sale and leaseback of equipment                                                -                 258
Proceeds from issuance of common stock                                                      45                 292
                                                                                   -----------          ----------  
        Net cash (used in) provided by financing activities                                (57)                228  
                                                                                   -----------          ----------  
                                                                                     
                                                                                     
Elimination of net cash activities of FASTech for the three                          
  months ended December 31, 1997                                                             -              (1,761)
                                                                                   -----------          ----------  

Effects of exchange rate changes on cash and cash equivalents                              133                (284)
                                                                                                                
                                                                                   -----------          ----------  
Net increase (decrease) in cash and cash equivalents                                     2,250              (2,598)
                                                                                                                  
                                                                                       
Cash and cash equivalents, beginning of period                                          68,161              75,253 
                                                                                   -----------          ----------  
                                                                                       
Cash and cash equivalents, end of period                                           $    70,411          $   72,655 
                                                                                   ===========          ==========  
</TABLE>

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


                                 Page 5 of 18
<PAGE>
 
                            BROOKS AUTOMATION, INC.
             NOTES TO CONDENSED 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 financial statements for the three
   months ended December 31, 1997, have been restated to reflect the fiscal 1998
   acquisition of FASTech Integration, Inc., which was accounted for under the
   pooling of interests method. Certain prior year's balances have been
   reclassified in order to conform to the current year's presentation. For
   further information, refer to the audited consolidated financial statements
   of the Company that are included in the Company's Annual Report on Form 10-K
   for the year ended September 30, 1998.

   The results of operations for the three months ended December 31, 1998, are
   not necessarily indicative of the results that may be expected for other
   quarters or the entire fiscal year.

 
2. Inventories
   -----------
<TABLE> 
<CAPTION> 
   Inventories consist of the following          December 31,  September 30,
   (in thousands):                                   1998           1998
                                                 ------------  -------------
   <S>                                            <C>             <C>        
    Raw materials and purchased parts                 $ 7,360        $ 8,815
    Work-in-process                                     7,037          7,878
    Finished goods                                      2,840          2,896
                                                      -------        -------
                                                      $17,237        $19,589
                                                      =======        =======
</TABLE>

3.  Earnings Per Share
    ------------------

    The following is a summary of the shares used in computing basic and diluted
    earnings per share (in thousands):
<TABLE>
<CAPTION>
                                                Three months ended December 31,
                                                        1998          1997
                                                      ------        ------
<S>                                               <C>            <C>       
  Weighted average shares outstanding
   used in computing basic earnings 
   per share                                          11,010        10,194
  Dilutive securities                                      -             -
                                                      ------        ------
  Shares used in computing diluted
   earnings per share                                 11,010        10,194
                                                      ======        ======
</TABLE>


4. Comprehensive Income
   --------------------

   The Company adopted SFAS No. 130, "Reporting Comprehensive Income" in the
   first quarter of fiscal 1999. SFAS No. 130 establishes new rules for the
   reporting and display of comprehensive income and its components. The
   adoption of SFAS 130 had no impact on the Company's net income or
   stockholders' equity. SFAS No. 130 requires the Company's foreign currency
   translation adjustments, which prior to adoption were reported separately in
   shareholders' equity, to be included in other comprehensive income. Total
   comprehensive loss, which was comprised of net loss and foreign currency
   translation adjustments, was $0.5 million and $3.6 million for the three
   months ended December 31, 1998 and 1997, respectively.

                                 Page 6 of 18
<PAGE>
 
                           BROOKS AUTOMATION, INC. 
             NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS 
                                  (unaudited)

5. Recent Accounting Pronouncements
   --------------------------------

   In June 1997, the Financial Accounting Standards Board ("FASB") issued SFAS
   No. 131, "Disclosures about Segments of an Enterprise and Related
   Information," which establishes standards for reporting information on
   operating segments in interim and annual financial statements. The statement
   is effective for the Company for fiscal 1999; however, the Company has no
   interim disclosure requirements in the year of adoption. Adoption of this
   statement will not have a material impact on the Company's results of
   operations or financial position.

   In June 1998, the FASB issued SFAS No. 133, "Accounting for Derivative
   Instruments and Hedging Activities." This statement is effective for all
   fiscal quarters of all fiscal years beginning after June 15, 1999 (fiscal
   2000 for the Company) and 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 No. 133 will
   not have a material impact on the Company's results of operations or
   financial position.

6. Significant Customers and Related Party Information
   ----------------------------------------------------

   For the three months ended December 31, 1998, the Company had revenues from
   two customers (not related parties) representing 20% and 16% of total
   revenues. For the three months ended December 31, 1997, the Company had
   revenues from a related party representing 16% of total revenues. At 
   December 31, 1998, accounts receivable from two customers (not related
   parties) accounted for 14% and 11% of total accounts receivable. At 
   September 30, 1998, accounts receivable from one customer (not a related
   party) represented 14% of total accounts receivable and accounts receivable
   from a related party represented 11% of total accounts receivable. Related
   party amounts included in accounts receivable are on standard terms and
   manner of settlement.

7. Contingency
   -----------

   There has been substantial litigation regarding patent and other intellectual
   property rights in the semiconductor and related industries. 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's patent
   counsel is investigating the claim, and 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. 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.

                                 Page 7 of 18
<PAGE>
 
                            BROOKS AUTOMATION, INC.

          ITEM 2.   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.

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, 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. In 1998 the Company acquired FASTech
Integration, Inc. ("FASTech"), a designer and supplier of top-to-bottom
integrated manufacturing execution system software solutions.

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's product revenues include sales of hardware and software products;
the Company's service revenues include revenue from maintenance contracts and
application consulting contracts.

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 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.

The Company's stock is currently quoted on the Nasdaq National Market under the
symbol "BRKS."

                                 Page 8 of 18
<PAGE>
 
RESULTS OF OPERATIONS

The following table sets forth certain financial data for the periods indicated
as a percentage of revenues:
<TABLE>
<CAPTION>
 
                                      For the three months ended December 31,
 
                                        1998                           1997
                                       --------                      ---------
<S>                                  <C>                            <C>    
Revenues:
   Product                                76.5%                          84.4%
   Services                               23.5%                          15.6% 
                                       --------                      ---------
      Total revenues                     100.0%                         100.0%
                                       ========                      =========
Gross profit:
   Product                                43.5%                          39.9%
   Services                               46.3%                          35.6%
      Total gross profit                  44.1%                          39.3% 
                                         
Operating expenses:
   Research and development               20.7%                          22.7%
   Selling, general and                                                     
    administrative                        28.9%                          23.9% 
                                       --------                      ---------

Loss from operations                      (5.5%)                         (7.3%)
                                                                               
Interest income                            3.9%                           3.2%  
                                 
Interest expense                          (0.2%)                         (0.9%)
                                       --------                      ---------

Loss before income taxes                  (1.8%)                         (5.0%)
                                      =========                     ==========
</TABLE>

THREE MONTHS ENDED DECEMBER 31, 1998, COMPARED WITH THREE MONTHS ENDED 
DECEMBER 31, 1997:

Revenues

Total revenues decreased 33.2% to $19.8 million for the three months ended
December 31, 1998, compared with revenues in the comparable quarter of the prior
fiscal year.  Product revenues decreased $9.9 million or 39.5% primarily as a
result of an $8.1 million decrease in hardware revenues and a $1.8 million
decrease in software revenues; and services revenues increased slightly to $4.7
million.  The decrease in product revenues was primarily the result of the
prolonged economic recession currently impacting the semiconductor industry and
related fabrication equipment sector.  Foreign revenues for the three months
ended December 31, 1998, were $11.9 million (60.2% of revenues) including $7.6
million of direct sales to Asian customers, compared with foreign revenues of
$10.6 million (35.7% of revenues), including $6.9 million of direct sales to
Asian customers in the comparable quarter of the prior fiscal year.  The Company
expects that foreign revenues will continue to account for a significant portion
of total revenues in fiscal 1999.  However, there can be no assurance that
foreign revenues particularly from Asia, which is suffering regional economic
downturns, will remain a strong component of the Company's total revenues.

Gross Profit

Overall, the gross profit as a percentage of total revenues increased to 44.1%
for the three months ended December 31, 1998, compared to 39.3%, in the
comparable quarter of the prior fiscal year.   The gross profit percentage for
product revenues was 43.5%, an increase from the 39.9% in the comparable quarter

                                 Page 9 of 18
<PAGE>
 
of the prior fiscal year primarily as a result of an improvement in the mix of
products sold and reductions in costs due to recently implemented cost controls.
The gross profit rate in the period is impacted by the mix of products sold
during the period.

The gross profit as a percentage of services revenues increased to 46.3% for the
three months ended December 31, 1998, as compared with 35.6% in the comparable
quarter of the prior fiscal year primarily as a result of cost reductions.
Included in the cost of services revenues are global support costs, which
consist primarily of personnel costs and travel expenses.

Research and Development

Research and development expenses decreased 39.3% to $4.1 million (20.7% of
revenues) for the three months ended December 31, 1998, from $6.7 million (22.7%
of revenues) in the comparable quarter of the prior fiscal year.  The decrease
in research and development expenses in the current quarter is due primarily to
lower personnel and personnel-related costs following a reduction in headcount
in the second and fourth quarters of fiscal 1998 and a reduction in incremental
spending, primarily consulting fees and other expenses incurred during the first
quarter of fiscal 1998 related to the launch of new atmospheric products and the
transition to the next generation of vacuum wafer handling products.

Selling, General and Administrative

Selling, general and administrative expenses decreased 19.1% to $5.7 million
(28.9% of revenues) for the three months ended December 31, 1998, from $7.1
million (23.9% of revenues) in the comparable quarter of the prior fiscal year.
The decrease in selling, general and administrative expenses is due primarily to
lower personnel and personnel-related costs following a reduction in headcount
in the second and fourth quarters of fiscal 1998 and expense control programs
initiated during the third and fourth quarters of fiscal 1998.
 
Interest Income and Interest Expense

Interest income decreased to $757,000 for the three months ended December 31,
1998, from $955,000 in the comparable quarter of the prior fiscal year.  The
decrease in interest income is primarily due to lower interest rates.  Interest
expense for the three months ended December 31, 1998, decreased to $33,000 from
$265,000 in the comparable period of the prior fiscal year primarily due to
the fact that most of the debt outstanding was repaid during fiscal 1998.
Included in the prior period's interest expense was $115,000 of deferred
financing costs resulting from the repayment of the related note payable and
interest on subordinated notes retired and capital leases repaid during fiscal
1998.

Income Tax Provision

The Company recorded a tax provision of $221,000 during the three months ended
December 31, 1998, primarily due to taxes on revenues and profits from foreign
operations.


LIQUIDITY AND CAPITAL RESOURCES

As of December 31, 1998, the Company's principal source of liquidity consisted
of $70.4 million in cash and cash equivalents, compared to $68.2 million at
September 30, 1998.  The Company had working capital of $99.3 million as of
December 31, 1998, compared to $99.9 million at September 30, 1998.

For the three months ended December 31, 1998, cash and cash equivalents
increased $2.2 million primarily as a result of $3.7 million in cash generated
by operating activities, partially offset by $1.6 million in cash used for
investing and financing activities.  The improvement in operating cash flow
resulted primarily from decreases in accounts receivable, inventory, and prepaid
expenses partially offset by a decrease in accounts payable and the Company's
net loss adjusted for noncash items.

The Company's primary investing activities encompassed capital spending
aggregating $1.3 million primarily for business information systems including
computer hardware and software, as well as headquarters facility improvements.
The Company expects to continue to make capital expenditures to support its
business activities.  Financing activities consisted primarily of repayments of
long-term debt and capital lease obligations.  The Company believes that current
cash and cash equivalent balances will be adequate to fund planned working 
capital and capital expenditure requirements for at least the next twelve 
months.

                                 Page 10 of 18
<PAGE>
 

YEAR 2000 READINESS

The year 2000 issue is the potential for system and processing failure of date-
related data as the result of computer-controlled systems using two digits
rather than four digits to define the applicable year. For example, computer
programs that have time-sensitive software may recognize a date using "00" as
the year 1900 rather than the year 2000. This could result in system failure or
miscalculations causing disruptions of operations, including, among other
things, a temporary inability to process transactions, send invoices, or engage
in similar normal business activities.

The Company may be affected by year 2000 issues related to noncompliant
information technology ("IT") systems or non-IT systems operated or sold by the
Company or by third parties.  The Company has substantially completed assessment
of its internal IT systems and non-IT systems.  At this point in its assessment,
the Company is not currently aware of any year 2000 problems relating to systems
operated or sold by the Company that would have a material adverse effect on the
Company's business, results of operations, or financial condition without taking
into account the Company's efforts to avoid such problems.

Although the Company believes that its systems are year 2000 compliant, the
Company utilizes third-party equipment and software that may not be year 2000
compliant.  In addition, the Company's products and software are often sold to
be integrated into or interfaced with third-party equipment or software. Failure
of third-party equipment or software to operate properly with regard to the year
2000 and thereafter could require the Company to incur unanticipated expenses to
remedy any problems, which could have a material adverse effect on the Company's
business, results of operations and financial condition.  The Company may also
be vulnerable to any failures by its major suppliers, service providers, and
customers to remedy their own internal IT and non-IT system year 2000 issues
which could, among other things, have a material adverse effect on the Company's
supplies and orders. At this time, the Company is unable to estimate the nature
or extent of any potential adverse impact resulting from the failure of third
parties, such as its suppliers, service providers and customers, to achieve year
2000 compliance. Moreover, such third parties, even if year 2000 compliant,
could experience difficulties resulting from year 2000 issues that may affect
its suppliers, service providers and customers. As a result, although the
Company does not currently anticipate that it will experience any material
shipment delays from its major product suppliers or any material sales delays
from its major customers due to year 2000 issues, there can be no assurance that
these third parties will not experience year 2000 problems or that any problems
would not have an adverse material effect on the Company's business, results of
operations and financial condition. Because the cost and timing of year 2000
compliance by third parties such as suppliers, service providers and customers
is not within the Company's control, the Company cannot give any assurance with
respect to the cost or timing of such efforts or any potential adverse effects
on the Company of any failure by these third parties to achieve year 2000
compliance.

The Company has no contingency plan in the event year 2000 problems relating to
its operations arise. The Company's failure to develop a contingency plan could
have a material adverse effect on the Company's business, results of operations
and financial condition.

To the extent that the Company does not identify any material non-compliant IT
systems or non-IT systems operated by the Company or by third parties, such as
the Company's suppliers, service providers and customers, the most reasonably
likely worst case year 2000 scenario is a systematic failure beyond the control
of the Company, such as a prolonged telecommunications or electrical failure, or
a general disruption in United States or global business activities that could
result in a significant economic downturn.  The Company believes that the
primary business risks, in the event of such failure or other disruption, would
include but not be limited to, loss of customers or orders, increased operating
costs, inability to obtain inventory on a timely basis, disruptions in product
shipments, or other business interruptions of a material nature, as well as
claims of mismanagement, misrepresentation, or breach of contract, any of which
could have a material adverse effect on the Company's business, results of
operations and financial condition.

                                 Page 11 of 18
<PAGE>
 
                             BROOKS AUTOMATION, INC.

             ITEM 3.   QUANTITATIVE AND QUALITATIVE DISCLOSURES
                               ABOUT MARKET RISK

                                        
INTEREST RATE EXPOSURE

Based on the Company's overall interest exposure at December 31, 1998, including
all interest rate sensitive instruments, a near-term change in interest rates
within a 95% confidence level based on historical interest rate movements would
not materially affect the consolidated results of operations or financial
position.


CURRENCY RATE EXPOSURE

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 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.


STOCK PRICE

The stock prices of semiconductor equipment companies are subject to significant
fluctuations. The stock price may be affected by a variety of factors that 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 12 of 18
<PAGE>
 
                            BROOKS AUTOMATION, INC.

                                  RISK FACTORS


FACTORS THAT MAY AFFECT FUTURE RESULTS

From time to time, information provided by the Company or statements made by its
employees may contain forward-looking information that involve substantial risks
and uncertainties that could cause actual results to differ materially from
targets or projected 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 and software products;
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 the 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 three months
ended December 31, 1998, and in fiscal 1998 and fiscal 1997 accounted for 66%,
61%, and 60% of total revenues, respectively.  In the three months ended
December 31, 1998, sales to two customers (not related parties) accounted for
20% and 16% of total revenues.  In fiscal 1998 and fiscal 1997, sales to Lam
Research Corporation (a related party), accounted 

                                 Page 13 of 18
<PAGE>
 
for 16% and 17% of the Company's total revenues, respectively. The Company's
customers generally do not enter into long-term agreements obligating them to
purchase the Company's products. A reduction or delay in orders from any
significant customer including reductions or delays due to market, economic or
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 three months ended December 31, 1998, and in fiscal 1998 and fiscal
1997, the Company derived 60%, 41%, and 38% 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, 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 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 


                                 Page 14 of 18
<PAGE>
 
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 MES and 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 are 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 Acquisitions

The Company completed the acquisition of FASTech on September 30, 1998, and
intends to pursue, from time to time, potential acquisitions of businesses,
products, and technologies that could complement or expand the Company's
business.  The combination of the Company and FASTech will require, among other
things, integration of the companies' respective products, technologies,
management information systems, distribution channels and key personnel, and the
coordination of their sales, marketing and research and development efforts.
There can be no assurance that such integration will be accomplished smoothly or
successfully, if at all.  If significant difficulties are encountered in the
integration of the existing products or technologies or the development of new
products and technologies, resources could be diverted from new product
development; and delays in new product introductions could occur.  The
integration of operations and technologies will require the dedication of
management and other personnel which may distract their attention from the day-
to-day business of the Company, the development or acquisition of new
technologies, and the pursuit of other business acquisition opportunities.
Failure to successfully accomplish the integration and development of the two
companies' operations and technologies would likely have a material adverse
effect on the Company's business, financial condition, and results of
operations.

The Company currently has no commitments or agreements with respect to any
material potential 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.

                                 Page 15 of 18
<PAGE>
 
Intellectual Property Protection and Related Contingency

The Company relies upon trade secrets and patents to protect its technology. Due
to the rapid technological change that characterizes the semiconductor and flat
panel display process equipment industries, the Company believes that the
improvement of existing technology, reliance upon trade secrets and unpatented
proprietary know-how and the development of new products may be more important
than patent protection in establishing and maintaining a competitive advantage.
It is the Company's policy to require all technical and management personnel to
enter into nondisclosure agreements.  Nevertheless, the Company has obtained
patents and will continue to make efforts to obtain patents, when available, in
connection with its product development program.  There can be no assurance that
any patent obtained will provide protection or be of commercial benefit to the
Company, or that its validity will not be challenged.   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 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.
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. No assurance can be given that any such patent application
will not have priority over patent applications filed by the Company.

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
infringement of patents then owned by General Signal, 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").
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 newly
acquired patents.  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 patented technology.  Such actions could be costly and
would divert the efforts and attention of the Company's management and technical
personnel, which would materially and adversely affect the Company's business,
financial condition and 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 16 of 18
<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

              The Company filed a Current Report on Form 8-K dated October 15,
              1998, reporting the acquisition of FASTech Integration, Inc.

                                 Page 17 of 18
<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.



February 15, 1999                           /s/ Robert J. Therrien            
- ----------------                           --------------------------------  
[Date]                                     Robert J. Therrien                
                                           Director and President            
                                           (Principal Executive Officer)     
                                                                             
February 15, 1999                          /s/ Ellen B. Richstone            
- -----------------                          --------------------------------  
[Date]                                     Ellen B. Richstone                
                                           Senior Vice President and         
                                           Chief Financial Officer           
                                           (Principal Financial Officer)     

                                 Page 18 of 18

<TABLE> <S> <C>

<PAGE>
<ARTICLE> 5
<LEGEND>
THIS SCHEDULE CONTAINS SUMMARY FINANCIAL INFORMATION EXTRACTED FROM DECEMBER 31,
1998 FORM 10Q, AND IS QUALIFIED IN ITS ENTIRETY BY REFERENCE TO SUCH FINANCIAL
STATEMENTS.
</LEGEND>
<MULTIPLIER> 1,000
       
<S>                             <C>
<PERIOD-TYPE>                   3-MOS
<FISCAL-YEAR-END>                          SEP-30-1999
<PERIOD-START>                             OCT-01-1998
<PERIOD-END>                               DEC-31-1998
<CASH>                                          70,411
<SECURITIES>                                         0
<RECEIVABLES>                                   20,558
<ALLOWANCES>                                     1,898
<INVENTORY>                                     17,237
<CURRENT-ASSETS>                               114,378
<PP&E>                                          40,972
<DEPRECIATION>                                  22,717
<TOTAL-ASSETS>                                 137,165
<CURRENT-LIABILITIES>                           15,076
<BONDS>                                              0
                                0
                                          0
<COMMON>                                           110
<OTHER-SE>                                     121,206
<TOTAL-LIABILITY-AND-EQUITY>                   137,165
<SALES>                                         15,155
<TOTAL-REVENUES>                                19,809
<CGS>                                            8,568
<TOTAL-COSTS>                                   11,068
<OTHER-EXPENSES>                                 9,819
<LOSS-PROVISION>                                     0
<INTEREST-EXPENSE>                                  33
<INCOME-PRETAX>                                   (354)
<INCOME-TAX>                                       221
<INCOME-CONTINUING>                               (575)
<DISCONTINUED>                                       0
<EXTRAORDINARY>                                      0
<CHANGES>                                            0
<NET-INCOME>                                      (575)
<EPS-PRIMARY>                                    (0.05)
<EPS-DILUTED>                                    (0.05)
        


</TABLE>


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