<PAGE>
                                                                   Exhibit 10.46

                           COMMERCIAL LEASE AGREEMENT

LESSOR    - KYUNGGI INDUSTRY
               REPRESENTATIVE - PARK, SANG CHEOUL

LESSEE    - BROOKS AUTOMATION ASIA LTD
               THERRIEN, ROBERT

This Commercial Lease Agreement ("Lease") is made and effective 10/01/1999, by
and between PARK, SANG CHEOUL: REPRESENTATIVE OF KYUNGGI INDUSTRY ("Lessor")
and BROOKS AUTOMATION ASIA, LTD. ("Lessee").

In consideration of the mutual covenant contained herein and other valuable
consideration received, and with the intent to be legally bound, the lessor and
the lessee agree as follows:

1.   ADDRESS

     398-1, komae - ri, kiheung - Eup, Youngin - City, Kyunggi - Do, Korea

     1st floor - 711.05m(2)
          2nd floor - 711.05m(2)
          4th floor - 711.05m(2)
          Total - 2133.15m(2)

2.   USE

<PAGE>
The Premises shall be used by the lessee solely for factory and office and for
activities incidental thereto. The lessee may not use the Leased Premises for
any other purpose without obtaining the prior written consent of the lessor.

3. MAINTENANCE

The lessee shall have an obligation of faithful maintenance to use the Leased
Premises (Front door, stairway, corridor, freight elevator, rest room, etc.)

4. TERM

   (1)   The lessor hereby leases the Leased Premises to the lessee, and the
         lessee hereby leases the same from the lessor, for an "Initial Term"
         beginning 10/01/1999 and ending 09/30/2001. Unless Either party may
         terminate this lease upon 1 month prior to the expiration of the
         Initial Term with a written notice to the other party, it is considered
         that this contract is extended to 2 years or more

   (2)   In case that the lessee haven't still used the Leased Premises since 2
         months passed from the beginning of the contract or the lessee don't
         deposit the key money(5-(1)) to lessor until the beginning of the
         contract, the lessor can cancel this contract unilaterally

   (3)   When the leassor or the lessee wants to terminate the contract by each
         party's circumstance in the middle of term or extended term, one must
         notify the intention of terminating the contract in written statement 3
         months prior to the other party. If the lessee pays 1-month lease
         payment and maintenance expenses for compensation to the lessor, the
         lessee can terminate the contract at any time.

   (4)   Both parties can't cancel only a portion of Leased Premises unless they
         reach an agreement

5. KEY MONEY

   (1)   Upon the execution of this Lease, the lessee shall pay The lessor a key
         money without liability for interest in the amount of (Won 150,000,000
         won) to be held as security for the payment of rent and the faithful
         performance by the lessee of all of its obligations in this lease. Of
         key money, earnest money (Won 75,000,000) must be put to the lessor at
         the time that contract is made, the rest (Won 75,000,000) must be put
         before the beginning date of contract

   (2)   If this contract is canceled by the clause 4.(2) or etc., earnest money
         passes to lessor as a penalty and the lessee can't demand to return
         earnest money

   (3)   The lessee can't use key money for monthly rental payment and also
         can't hand the right of return claim for key money over the third party
         or hand the right of return claim as the right of security over the
         third party

6. MONTHLY RENTAL PAYMENT
<PAGE>
   (1) The lessee shall pay a monthly rental payment (Won 9,000,000) to the
       lessor in the 30th day of each calendar month (if 30th day is holiday, it
       shall be following day)

   (2) The rental payment amount for any partial calendar months included in the
       lease term shall be prorated on a daily basis

7. MAINTENANCE EXPENSES

   (1) The lessee shall pay maintenance expenses (electrical charges, water
       supply and drainage charges, air cooling and heating charges, ventilation
       charges, cleaning charges) with monthly rental payment in the 30th day of
       each month

   (2) The lessee also shall pay additional maintenance expenses caused by the
       lessee except the basic maintenance expenses according to the lessor's
       basis

8. FEE ADJUSTMENT

   Among the term of contract (4. (1)) or the extended term, the lessor can
   adjust the key money, monthly rental payment and maintenance expenses through
   notifying one-month prior as follows ((1)-(3)). Adjusted key money, monthly
   rental payment and maintenance expenses are applied from the 1st day of the
   following month

   (1) In case that tax of the Leased Premises or lease management is remarkably
       increased or increase is expected

   (2) In case that maintenance expenses is remarkably increased

   (3) In case that the prices rise or economical circumstance is highly changed

9. EFFECTIVE DATE OF RENTAL PAYMENT

   If the lessee can't use the Leased Premises for the lessor's certain reason
   from starting date of the contract, real date the lessee uses the Leased
   Premises must be considered when paying monthly rental payment

10. LATE CHARGE

   If lessee fails to pay key money, monthly rental payment or any other amount
   due hereunder within the time limit of payment, lessee shall pay lessor a
   late payment charge equal to annual interest of 19% of the overdue amounts.

11. RETURNING KEY MONEY

   In case of expiration or termination of this contract, the lessor shall give
   back key money to the lessee within 7 days after the lessee recedes the
   Leased Premises

   If the lessee has got miscellaneous expenses or debts to pay to the lessor,
   the lessor returns key money after deducting miscellaneous expenses or debts

12. INSURANCE

   (1) If the Leased Premises or any other part of the Building is damaged by
       fire resulting from any act or negligence of the lessee or any of
       lessee's agents, employees or invitees, the lessee shall pay extended
       coverage insurance to the
<PAGE>
     (2) To avoid a conflict resulting from loss of each party's (the lessor and
         the lessee) own Property by the fire, the lessee shall, at its own
         expense, be insured for comprehensive general liability with respect to
         the Leased Premises and the lessee shall provide the lessor with
         current Certificates of comprehensive general liability Insurance

13. VALUE ADDED TAX

    The lessee shall cover value added tax coming from this contract

14. ALTERATION

     (1) With a prior written consent of lessor, the lessee, at its own
         expenses, can do as follows (A, B)

     A.  Attachment or alteration of Interior facilities, partitions and
         advertising objects

     B.  Establishment or moving of miscellaneous facilities and power supply
         facilities or establishment, extension, moving or alteration of water
         supply and drainage facilities

     (2) The lessee, at its own expenses, shall restore the former condition of
         the Leased premises after expiration

     (3) If the lessee doesn't perform his duty to restore the Leased premises
         or the lessor don't approve lessee's restoration, the lessor can deduct
         additional expenses needed to restore the Leased premises in the key
         money.

15. CESSION AND SUBLEASE

    The lessee can't hand rights and duties of lease contract over the third
    party and also sublease all or any part of the Leased Premises

16. PROPERTY PROTECTION

    The lessee is responsible for the safety maintenance of the lessee's
    property and the lessor is not responsible for accident (robbery, fire and
    etc.) that happened in the Leased Premises

17. EXEMPTION

     (1) The lessor is not responsible for all the damage by legally
         irresistible accident beyond the human control (earthquake, storms and
         floods, war, riot and etc.)

     (2) The lessor is not responsible for governmental restrictions caused by
         the lessee's alteration, remodeling or maintenance

18. CHANGE OF OWNERSHIP

    Even if proprietary, right of management and ownership are changed, this
    contract still has a legal force and Next lessor shall faithfully abide by
    this






<PAGE>



19.  CHANGE OF LESSEE'S INFORMATION

     If there is a change in the lessee's information (address, company name,
     representative, company capital, matters required to be registered and
     etc), the lessee shall notify the lessor of a change without delay

20.  INDEMNIFICATION

     If the lessee does damage to the body or property of the lessor or third
     party with or without an intention, the lessee shall notify the lessor of
     this without delay and also pay for damage

21.  CONTRACT TERMINATION

     (1)  The lessor can immediately terminate this contract if the lessee
          conduct the below clauses

     A.   In case the monthly rental payment and maintenance expenses are two
          months overdue

     B.   Distraint, provisional distraint, provisional disposition, auction or
          bankruptcy of the lessee's property coming from liability can cause
          contract termination by the lessor's judgment

     C.   In case that The lessee violates any clause in this contract

     (2)  In case of above clauses (A - C), the lessor can terminate this
          contract at any time and take back Leased Premises and go through
          legal formalities. The fact that the lessor has key money can't be
          the reason that the lessee refuses to return the Leased Premised

22.  EVACUATION AND RESTORATION

     (1)  The lessee shall evacuate the Leased Premises within an expiration
          date and return all properties of the lessor when contract is expired

     (2)  The lessee, at its own expenses, shall restore the Leased Premises to
          the original conditions within expiration date (ordinary wear and tear
          excepted)

     (3)  In case that the lessee didn't evacuate the Leased Premises and
          restore the Leased Premises to the original conditions within an
          expiration date, the lessee shall pay additional charges (monthly
          rental payments and maintenance expenses) until the evacuation and
          restoration are finished. The lessee is responsible for all matters
          caused by delay of the evacuation and restoration

23.  APPLICATORY LAW

     Details excepting the clause of this contract apply to the law of Republic
     of Korea and customary laws of lease



<PAGE>
     In case that a dispute arises on the matters of this contract, basis is
     the contract written in Korean

25.  REGISTRATION

     The lessor shall register lease contract in the proper form and the lessee
     shall pay registration fee to the lessor

26.  EXTENSION OF GUARDROOM

     After obtaining the permission from the competent authorities, the lessor
     shall pay all expenses needed to extend the guardroom

27.  JURISDICTION

     The lawsuit of this contract is under a competent local court

To attest a conclusion of this contract, make out a contract in duplicate with
a signature of each party and each party keeps this contract


                                   03/31/2000


The lessor: 398-1, komae-ri, kiheung-eup, Yongin-city, Kyunggi-do, Korea

     Representative of Kyunggi Industry

     Park, Sang Cheoul

The lessee: 398-1, komae-ri, kiheung-eup, Yongin-city, Kyunggi-do, Korea

     C.E.O. of Brooks Automation Asia

     Therrien, Robert