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

                                  SCHEDULE 13D
                        Under the Securities Act of 1934
                                (Amendment No. 3)

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

                                December 29, 2005
             (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. (David Nierenberg is president of the General
     Partner, which is Nierenberg Investment Management Company.)
--------------------------------------------------------------------------------
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
                    
                    1,769,532 Common shares (2.4%)
               -----------------------------------------------------------------
  NUMBER OF    8    SHARED VOTING POWER
   SHARES           
BENEFICIALLY        0
  OWNED BY     -----------------------------------------------------------------
    EACH       9    SOLE DISPOSITIVE POWER
  REPORTING         
   PERSON           1,769,532
    WITH       -----------------------------------------------------------------
               10   SHARED DISPOSITIVE POWER
                    
                    0
--------------------------------------------------------------------------------
11   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

     3,728,802 shares (5.0%)
--------------------------------------------------------------------------------
12   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES*  |_|


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

     5.0%
--------------------------------------------------------------------------------
14   TYPE OF REPORTING PERSON*

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



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

     The D3 Family Retirement Fund, L.P. (David Nierenberg is president of the
     General Partner, which is Nierenberg Investment Management Company.)
--------------------------------------------------------------------------------
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
                    
                    579,500 common shares (0.8%)
               -----------------------------------------------------------------
  NUMBER OF    8    SHARED VOTING POWER
   SHARES           
BENEFICIALLY        0
  OWNED BY     -----------------------------------------------------------------
    EACH       9    SOLE DISPOSITIVE POWER
  REPORTING         
   PERSON           579,500
    WITH       -----------------------------------------------------------------
               10   SHARED DISPOSITIVE POWER
                    
                    0
--------------------------------------------------------------------------------
11   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

     3,728,802 shares (5.0%)
--------------------------------------------------------------------------------
12   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES*  |_|


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

     5.0%
--------------------------------------------------------------------------------
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 Children's Fund, L.P. (David Nierenberg is president of the General
     Partner, which is Nierenberg Investment Management Company.)
--------------------------------------------------------------------------------
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
                    
                    158,860 common shares (0.2%)
               -----------------------------------------------------------------
  NUMBER OF    8    SHARED VOTING POWER
   SHARES           
BENEFICIALLY        0
  OWNED BY     -----------------------------------------------------------------
    EACH       9    SOLE DISPOSITIVE POWER
  REPORTING         
   PERSON           158,860
    WITH       -----------------------------------------------------------------
               10   SHARED DISPOSITIVE POWER
                    
                    0
--------------------------------------------------------------------------------
11   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

     3,728,802 shares (5.0%)
--------------------------------------------------------------------------------
12   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES*  |_|


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

     5.0%
--------------------------------------------------------------------------------
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

     The D3 Offshore Fund, L.P. (David Nierenberg is president of the General
     Partner, which is Nierenberg Investment Management Company.)
--------------------------------------------------------------------------------
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
                    
                    865,660 common shares (1.2%)
               -----------------------------------------------------------------
  NUMBER OF    8    SHARED VOTING POWER
   SHARES           
BENEFICIALLY        0
  OWNED BY     -----------------------------------------------------------------
    EACH       9    SOLE DISPOSITIVE POWER
  REPORTING         
   PERSON           865,660
    WITH       -----------------------------------------------------------------
               10   SHARED DISPOSITIVE POWER
                    
                    0
--------------------------------------------------------------------------------
11   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

     3,728,802 shares (5.0%)
--------------------------------------------------------------------------------
12   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES*  |_|


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

     5.0%
--------------------------------------------------------------------------------
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

     The D3 Family Bulldog Fund, L.P. (David Nierenberg is president of the
     General Partner, which is Nierenberg Investment Management Company.)
--------------------------------------------------------------------------------
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
                    
                    355,250 common shares (0.5%)
               -----------------------------------------------------------------
  NUMBER OF    8    SHARED VOTING POWER
   SHARES           
BENEFICIALLY        0
  OWNED BY     -----------------------------------------------------------------
    EACH       9    SOLE DISPOSITIVE POWER
  REPORTING         
   PERSON           355,250
    WITH       -----------------------------------------------------------------
               10   SHARED DISPOSITIVE POWER
                    
                    0
--------------------------------------------------------------------------------
11   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

     3,728,802 shares (5.0%)
--------------------------------------------------------------------------------
12   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES*  |_|


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

     5.0%
--------------------------------------------------------------------------------
14   TYPE OF REPORTING PERSON*

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


                                       6


Item 1.     Security and Issuer.

            Common stock in BROOKS  AUTOMATION,  INC. (BRKS) 15 Elizabeth Drive,
            Chelmsford, MA 01824-4111.

Item 2.     Identity and Background.

            The D3 Family Funds are Washington State limited partnerships, whose
            principal  business is investing in the equities of public micro-cap
            issuers.  The D3 Family Funds  consist of: D3 Family  Fund,  L.P, D3
            Family  Retirement  Fund, L.P, D3 Children's  Fund, L.P, D3 Offshore
            Fund,  L.P., D3 Family Bulldog Fund, L.P.  Located at 19605 N.E. 8th
            St.,  Camas,  Washington  98607.  No convictions  or  administrative
            proceedings as described in 2 (d) and (e).

Item 3.     Source and Amount of Funds or Other Consideration

            Source  of funds  is  money  invested  in the  partnership  by their
            partners.

Item 4.     Purpose of Transaction

            On December 29, we bought  580,000 more shares of BRKS,  raising our
            aggregate  ownership back to 5%. We believe that this purchase makes
            us BRKS' second largest shareholder.

            Both factors  mentioned in our prior 13D filing,  dated  December 9,
            2005, plus a third factor,  created this buying opportunity.  First,
            some former Helix  shareholders  have been selling their BRKS shares
            either  because they had achieved  their  investment  objectives  or
            because they only hold stocks which pay dividends.  We believe,  for
            example,  that Helix' largest  shareholder,  which obtained nearly 8
            million  BRKS  shares  in  exchange  for its Helix  shares,  now has
            disposed of the  majority of their BRKS  shares.  Second,  some BRKS
            shareholders  sold their shares out of frustration  with the erratic
            recent  performance of BRKS' software  division.  Third,  and due in
            part to the two abovementioned  factors, some BRKS shareholders have
            been selling their shares to realize income tax losses,  since BRKS'
            share price (as of this instant) fell 26% this year and 46% over the
            last two years,  (despite the  substantial  operating  and strategic
            progress made by the company.)

            Fortunately  for those of us who want to be shareholders of BRKS--as
            it  gains  market  share  in  its  core  business  of  robotic  tool
            automation  systems and service,  as it penetrates more Tier One OEM
            accounts,  and as it  continues  reducing  the costs of the combined
            companies and generating  free cash--we  believe that the short term
            selling pressure on the stock price is now over. We believe this for
            the following reasons:

            1.    2005 tax loss selling ends December 30.


                                       7


            2.    We believe that most selling by former  shareholders  of Helix
                  is over.

            3.    The  performance  of  BRKS'  software  division  should  begin
                  showing substantial improvement because BRKS has sharpened its
                  strategic focus and right-sized the division's  costs. We also
                  hope the division will have improved governance and oversight.

            4.    We are encouraged by Christmas retail sales,  which augur well
                  for the  semiconductor  industry and for BRKS as one its major
                  equipment  suppliers.  According to  SpendingPulse,  aggregate
                  retail  sales  through   December  24  rose  8.7%  over  2004,
                  considerably  higher than had been  forecast  and greater than
                  2004's  6.7% gain,  even in the face of higher fuel prices and
                  the pricking of the housing bubble. Consumer electronics sales
                  grew  even  faster,  up 11% over  2004,  and  were the  second
                  fastest  growing product  category.  We believe that consumers
                  have not yet completed their electronics  buying.  Substantial
                  unmet demand remains, for example, for Microsoft's XBOX gaming
                  machine  and for  Apple's  iPod Nano.  And we are in the early
                  stages  of a  major  replacement  cycle  of  television  sets.
                  Instead of furloughing capacity, as they did at this time last
                  year, we would expect semiconductor fabs to continue investing
                  in manufacturing equipment.

            Finally,  on the  subject of BRKS'  corporate  governance,  which we
            touched on lightly in our prior 13D,  we have had no  response  from
            BRKS'  Board  of  Directors  to  our  November  17  letter.  We  are
            disappointed  by 1 1/2 months of silence,  both  because the tone of
            our  letter was  constructive  and  because  BRKS'  board  expressly
            "encourage[d]" communications from shareholders in their 2005 annual
            meeting  proxy  statement  (see page 8 of the  proxy).  A timely and
            detailed  response could have  substantiated,  rather than undercut,
            this invitation.

            In our  November  17 letter  we set  forth our views on the  optimal
            size,  composition,  and  leadership  of BRKS'  Board of  Directors.
            Because  BRKS'  fiscal  year ended  September  30, and  because  the
            company filed its 2005 annual meeting proxy with the SEC immediately
            after the  holidays,  on January 6, 2005,  we believe that the proxy
            for the 2006 annual  meeting may be imminent.  We hope that,  in the
            absence of a  substantive  response  to our  letter,  the proxy will
            demonstrate  tangible progress on the governance issues which we and
            other large outside shareholders care about.

            If we are not satisfied with what we read in the proxy, with respect
            to these  issues,  we  reserve  the  right  to  contact  other  BRKS
            shareholders  using a proxy statement and proxy solicitation firm of
            our own.  Unfortunately,  this would  bring the issues  which we had
            hoped to resolve privately into the public domain. Since we strongly
            would prefer for BRKS to remain focused on integrating Helix, fixing
            BRKS software, and gaining market share in its core business of tool
            automation, we hope that the issues we raised still will be resolved
            in a friendly,  private manner.  But with the clock ticking down the
            end of 2005,  and in the absence of a response from the company,  we
            feel obligated to begin preparing for other possibilities.


                                       8


Item 5.     Interest in Securities of the Issuer.

            (a,b) D3 Family Funds own and have sole voting and dispositive power
                  over 3,728,802, 5.0% common shares of BRKS.

            (c)



                                                       Transaction           Shares
                  Fund                                     Date               Bought        Price
                                                                                     
                  D3 Family Fund, L.P.                  10/27/2005            70,000        11.99
                  D3 Family Fund, L.P.                  10/28/2005            17,700        11.64
                  D3 Family Fund, L.P.                  12/29/2005           242,500        12.46
                  D3 Family Retirement Fund, L.P.       12/29/2005           125,500        12.46
                  D3 Children's Fund, L.P.              10/28/2005            12,000        11.64
                  D3 Children's Fund, L.P.              12/29/2005            42,500        12.46
                  D3 Offshore Fund, L.P.                10/27/2005            42,500        11.99
                  D3 Offshore Fund, L.P.                12/29/2005           115,500        12.46
                  D3 Family Bulldog Fund, L.P.          10/27/2005            50,000        11.99
                  D3 Family Bulldog Fund, L.P.          10/28/2005            25,000        11.64
                  D3 Family Bulldog Fund, L.P.          12/29/2005            54,000        12.46


            (d)   N/A

            (e)   N/A

Item 6.     Contracts,   Arrangements,   Understandings  or  Relationships  with
            Respect to Securities of the Issuer.

            N/A

Item 7.     Material to be Filed as Exhibits

            N/A

                                    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.


December 29, 2005                          /s/ DAVID NIERENBERG
-----------------                          -------------------------------------
                                           David Nierenberg
                                           President
                                           Nierenberg Investment Management
                                           Company, Inc., the General Partner of
                                           The D3 Family Funds


                                       9