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

                                  SCHEDULE 13D
                    Under the Securities Exchange Act of 1934
                                (Amendment No. 6)

                         BROOKS AUTOMATION, INC. (BRKS)
                                (Name of Issuer)

                                  Common Stock
                         (Title of Class of Securities)

                                    114340102
                                 (CUSIP Number)

                                David Nierenberg
                               The D3 Family Funds
                               19605 NE 8th Street
                                 Camas, WA 98607
                                 (360) 604-8600

                                 With a copy to:

                               Henry Lesser, Esq.
                                DLA Piper US LLP
                             2000 University Avenue
                            East Palo Alto, CA 94303
                                 (650) 833-2000

                  (Name, Address and Telephone Number of Person
                Authorized to Receive Notices and Communications)

                                January 29, 2007
             (Date of Event which Requires Filing of this Statement)

If the filing person has previously filed a statement on Schedule 13G to report
the acquisition that is the subject of this Schedule 13D and is filing this
schedule because of ss.ss. 240.13d-1(e), 240.13d-1(f) or 240.13d-1(g), check the
following box |_|.



--------------------------------------------------------------------------------
1    NAME OF REPORTING PERSON
     S.S. OR I.R.S. IDENTIFICATION NOS. OF ABOVE PERSON

     The D3 Family Fund, L.P.
--------------------------------------------------------------------------------
2    CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                                 (a)  |X|
                                                                 (b)  |_|
--------------------------------------------------------------------------------
3    SEC USE ONLY


--------------------------------------------------------------------------------
4    SOURCE OF FUNDS*

     WC
--------------------------------------------------------------------------------
5    CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED
     PURSUANT TO ITEMS 2(d) OR 2(e)                                   |_|


--------------------------------------------------------------------------------
6    CITIZENSHIP OR PLACE OF ORGANIZATION

     Washington
--------------------------------------------------------------------------------
               7    SOLE VOTING POWER

                    849,215 Common shares (1.1%)
               -----------------------------------------------------------------
  NUMBER OF    8    SHARED VOTING POWER
   SHARES
BENEFICIALLY        0
  OWNED BY     -----------------------------------------------------------------
    EACH       9    SOLE DISPOSITIVE POWER
  REPORTING
   PERSON           849,215
    WITH       -----------------------------------------------------------------
               10   SHARED DISPOSITIVE POWER

                    0
--------------------------------------------------------------------------------
11   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

     For the reporting person listed on this page, 849,215; for all
     reporting persons as a group, 4,847,458 shares (6.4%)
--------------------------------------------------------------------------------
12   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES*  |_|


--------------------------------------------------------------------------------
13   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)

     6.4%
--------------------------------------------------------------------------------
14   TYPE OF REPORTING PERSON*

     PN
--------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!


                                       2


--------------------------------------------------------------------------------
1    NAME OF REPORTING PERSON
     S.S. OR I.R.S. IDENTIFICATION NOS. OF ABOVE PERSON

     The DIII Offshore Fund, L.P.
--------------------------------------------------------------------------------
2    CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                                 (a)  |X|
                                                                 (b)  |_|
--------------------------------------------------------------------------------
3    SEC USE ONLY


--------------------------------------------------------------------------------
4    SOURCE OF FUNDS*

     WC
--------------------------------------------------------------------------------
5    CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED
     PURSUANT TO ITEMS 2(d) OR 2(e)                                   |_|


--------------------------------------------------------------------------------
6    CITIZENSHIP OR PLACE OF ORGANIZATION

     Bahamas
--------------------------------------------------------------------------------
               7    SOLE VOTING POWER

                    1,106,718 common shares (1.5%)
               -----------------------------------------------------------------
  NUMBER OF    8    SHARED VOTING POWER
   SHARES
BENEFICIALLY        0
  OWNED BY     -----------------------------------------------------------------
    EACH       9    SOLE DISPOSITIVE POWER
  REPORTING
   PERSON           1,106,718
    WITH       -----------------------------------------------------------------
               10   SHARED DISPOSITIVE POWER

                    0
--------------------------------------------------------------------------------
11   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

     For the reporting person listed on this page, 1,106,718; for all
     reporting persons as a group, 4,847,458 shares (6.4%)
--------------------------------------------------------------------------------
12   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES*  |_|


--------------------------------------------------------------------------------
13   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)

     6.4%
--------------------------------------------------------------------------------
14   TYPE OF REPORTING PERSON*

     PN
--------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!


                                       3


--------------------------------------------------------------------------------
1    NAME OF REPORTING PERSON
     S.S. OR I.R.S. IDENTIFICATION NOS. OF ABOVE PERSON

     The D3 Family Bulldog Fund, L.P.
--------------------------------------------------------------------------------
2    CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                                 (a)  |X|
                                                                 (b)  |_|
--------------------------------------------------------------------------------
3    SEC USE ONLY


--------------------------------------------------------------------------------
4    SOURCE OF FUNDS*

     WC
--------------------------------------------------------------------------------
5    CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED
     PURSUANT TO ITEMS 2(d) OR 2(e)                                   |_|


--------------------------------------------------------------------------------
6    CITIZENSHIP OR PLACE OF ORGANIZATION

     Washington
--------------------------------------------------------------------------------
               7    SOLE VOTING POWER

                    2,891,525 common shares (3.8%)
               -----------------------------------------------------------------
  NUMBER OF    8    SHARED VOTING POWER
   SHARES
BENEFICIALLY        0
  OWNED BY     -----------------------------------------------------------------
    EACH       9    SOLE DISPOSITIVE POWER
  REPORTING
   PERSON           2,891,525
    WITH       -----------------------------------------------------------------
               10   SHARED DISPOSITIVE POWER

                    0
--------------------------------------------------------------------------------
11   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

     For the reporting person listed on this page, 2,891,525; for all
     reporting persons as a group, 4,847,458 shares (6.4%)
--------------------------------------------------------------------------------
12   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES*  |_|


--------------------------------------------------------------------------------
13   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)

     6.4%
--------------------------------------------------------------------------------
14   TYPE OF REPORTING PERSON*

     PN
--------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!


                                       4


--------------------------------------------------------------------------------
1    NAME OF REPORTING PERSON
     S.S. OR I.R.S. IDENTIFICATION NOS. OF ABOVE PERSON

     Nierenberg Investment Management Company, Inc.
--------------------------------------------------------------------------------
2    CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                                 (a)  |X|
                                                                 (b)  |_|
--------------------------------------------------------------------------------
3    SEC USE ONLY


--------------------------------------------------------------------------------
4    SOURCE OF FUNDS*

     WC
--------------------------------------------------------------------------------
5    CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED
     PURSUANT TO ITEMS 2(d) OR 2(e)                                   |_|


--------------------------------------------------------------------------------
6    CITIZENSHIP OR PLACE OF ORGANIZATION

     Washington
--------------------------------------------------------------------------------
               7    SOLE VOTING POWER

                    0
               -----------------------------------------------------------------
  NUMBER OF    8    SHARED VOTING POWER
   SHARES
BENEFICIALLY        4,847,458 shares (6.4%)
  OWNED BY     -----------------------------------------------------------------
    EACH       9    SOLE DISPOSITIVE POWER
  REPORTING
   PERSON           0
    WITH       -----------------------------------------------------------------
               10   SHARED DISPOSITIVE POWER

                    4,847,458 shares
--------------------------------------------------------------------------------
11   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

     For the reporting person listed on this page, 4,847,458; for all
     reporting persons as a group, 4,847,458 shares (6.4%)
--------------------------------------------------------------------------------
12   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES*  |_|


--------------------------------------------------------------------------------
13   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)

     6.4%
--------------------------------------------------------------------------------
14   TYPE OF REPORTING PERSON*

     PN
--------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!


                                       5



--------------------------------------------------------------------------------
1    NAME OF REPORTING PERSON
     S.S. OR I.R.S. IDENTIFICATION NOS. OF ABOVE PERSON

     Nierenberg Investment Management Offshore, Inc.
--------------------------------------------------------------------------------
2    CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                                 (a)  |X|
                                                                 (b)  |_|
--------------------------------------------------------------------------------
3    SEC USE ONLY


--------------------------------------------------------------------------------
4    SOURCE OF FUNDS*

     WC
--------------------------------------------------------------------------------
5    CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED
     PURSUANT TO ITEMS 2(d) OR 2(e)                                   |_|


--------------------------------------------------------------------------------
6    CITIZENSHIP OR PLACE OF ORGANIZATION

     Bahamas
--------------------------------------------------------------------------------
               7    SOLE VOTING POWER

                    0
               -----------------------------------------------------------------
  NUMBER OF    8    SHARED VOTING POWER
   SHARES
BENEFICIALLY        1,106,718 common shares (1.5%)
  OWNED BY     -----------------------------------------------------------------
    EACH       9    SOLE DISPOSITIVE POWER
  REPORTING
   PERSON           0
    WITH       -----------------------------------------------------------------
               10   SHARED DISPOSITIVE POWER

                    1,106,718 common shares
--------------------------------------------------------------------------------
11   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

     For the reporting person listed on this page, 1,106,718; for all
     reporting persons as a group, 4,847,458 shares (6.4%)
--------------------------------------------------------------------------------
12   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES*  |_|


--------------------------------------------------------------------------------
13   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)

     6.4%
--------------------------------------------------------------------------------
14   TYPE OF REPORTING PERSON*

     PN
--------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!


                                       6


      This  Amendment  No. 6 to  Schedule  13D  (this  "Amendment")  amends  the
below-indicated  items from the Schedule 13D previously filed by or on behalf of
the undersigned  parties (the "Reporting  Persons"),  as previously amended (the
"Schedule 13D"), by supplementing such Items with the information below:

Item 4. Purpose of Transaction

Recently   Institutional   Shareholder  Services  (ISS)  and  Glass  Lewis  (GL)
recommended  that clients  withhold  their votes from several  incumbent  Brooks
Automation (BRKS) directors. We strongly disagree with ISS and GL and have voted
all of our shares enthusiastically to re-elect the entire BRKS director slate.

We believe that the Board of Directors  of BRKS has  improved  dramatically  the
quality of its corporate governance in the past year. First, the Board announced
that former  Chairman  and CEO Robert  Therrien  would not be  re-nominated  for
another term on the Board.  Second, when the Wall Street Journal broke the story
last March about the  appearance of  back-dated  stock option grants made to Mr.
Therrien,  the  Board  immediately  appointed  a  special  committee  of  newer,
independent  directors to examine the matter and empowered the special committee
to engage independent legal and accounting counsel.  Later, after several months
of intensive  examination of the Therrien and other suspect stock option grants,
the two board  members who had been the Board's  compensation  committee  at the
time the Therrien  grants were made resigned  from the Board of  Directors.  Now
BRKS'  Board has a capable new Chair;  the former Lead  Director is no longer on
the Board;  and BRKS'  compensation  committee and its nominating and governance
committee also have new Chairs. The company is publicly committed to cooperating
fully with federal  examinations of past option practices and to never repeating
the unfortunate practices of the past. Fundamentally, we believe that BRKS has a
strong balance sheet, a sensible corporate strategy, and excellent management to
execute the strategy.

None of the  directors  opposed  by ISS and GL served on the BRKS Board when the
problematic  stock options were granted to the former Chairman and CEO. In fact,
directors  Robert  Lepofsky and Mark Wrighton did not join BRKS' Board until the
company acquired Helix  Technology late in 2005.  Director Krishna Palepu joined
the  Board at about  the same time  precisely  to  improve  the  quality  of its
governance.

In conclusion,  we have voted  enthusiastically  to re-elect all eight incumbent
BRKS  directors.  We believe  that the  formulaic  approach  taken by ISS and GL
would,  if  followed in this case,  cause  shareholders  to withhold  votes from
directors who have been doing difficult work exceptionally well. We believe that
doing the right thing should be rewarded, not punished.

By reporting the information contained in this Amendment,  the Reporting Persons
do not intend to solicit, nor are they soliciting, proxies or consents from, nor
seeking or  requesting  any other  action by, any of the other  stockholders  of
BRKS. The Reporting  Persons are reporting  their own voting  intentions and the
reasons therefor.

The previous  statements by the Reporting  Persons regarding their investment in
BRKS   represent   solely   their  own   analyses   and   judgments,   based  on
publicly-available  information and their own


                                       7


internal evaluation thereof.  Those statements are not intended,  and should not
be  relied  on,  as  investment  advice to any  other  investor  or  prospective
investor.  To the extent those statements reflect assessments of possible future
developments,  those  assessments  are inherently  subject to the  uncertainties
associated  with all  assessments  of future  events;  actual  developments  may
materially  differ as a result of circumstances  affecting BRKS and/or extrinsic
factors  such  as  developments  in the  company's  industry  and  the  economic
environment.  The Reporting  Persons  reserve the right to change their internal
evaluation of this investment in the future,  as well as to increase or decrease
their  investment  depending on their  evaluation,  without further amending the
Schedule 13D except as required by applicable rules.

Item 5. Interest in Securities of the Issuer.

      (a, b) The Reporting Persons, in the aggregate, beneficially own 4,847,458
Shares, constituting approximately 6.4% of the outstanding Shares.

      (c) During the past sixty (60) days,  the  following  purchases  of Shares
were made by D3 Family Funds in open market transactions:

       Fund                        Trade Date    Shares Bought           Price
       ----                        ----------    -------------           -----
       DIII Offshore Fund LP       1/18/2007         147,000             14.00
       D3 Family Bulldog Fund LP   1/18/2007           3,000             13.97

In addition, on January 3, 2007, an aggregate of 203,280 Shares were distributed
in kind, on a pro rate basis, to the general partners in the DIII Offshore Fund,
LP.

Item 7. Material to be filed as Exhibits

      Exhibit 1 to this  Amendment  is the joint  filing  agreement  pursuant to
which all of the filing persons have  authorized the filing of this Amendment as
a group.


                                       8


         SIGNATURE

After reasonable inquiry and to the best of my knowledge and belief, each of the
undersigned  certifies that the  information set forth in the Statement is true,
complete and correct.

                                 D3 Family Fund, L.P. and D3 Bulldog
                                 Fund, L.P
                                 By: Nierenberg Investment Management
                                      Company, Inc.

                                 Its: General Partner


January 29, 2007                 By: /s/ David Nierenberg
                                 -----------------------------------
                                         David Nierenberg, President


                                 DIII Offshore Fund, L.P.

                                 By: Nierenberg Investment Management
                                      Offshore, Inc.

                                 Its: General Partner


January 29, 2007                 By: /s/ David Nierenberg
                                 -----------------------------------
                                         David Nierenberg, President


                                 Nierenberg Investment Management
                                      Company, Inc.


January 29, 2007                 By: /s/ David Nierenberg
                                 -----------------------------------
                                         David Nierenberg, President

                                 Nierenberg Investment Management
                                      Offshore, Inc.


January 29, 2007                 By: /s/ David Nierenberg
                                 ------------------------------------
                                         David Nierenberg, President


                                       9