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Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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MIC-Info: RSA-MD5,RSA,
 NrwujF251TzXOBLEzihIWzzjvVgGGH1BuTW9ARqY8SDwkgq1DAYruefe5QNvuHA7
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<SEC-DOCUMENT>0001209191-07-071340.txt : 20071221
<SEC-HEADER>0001209191-07-071340.hdr.sgml : 20071221
<ACCEPTANCE-DATETIME>20071221123440
ACCESSION NUMBER:		0001209191-07-071340
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20071220
FILED AS OF DATE:		20071221
DATE AS OF CHANGE:		20071221

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			BROOKS AUTOMATION INC
		CENTRAL INDEX KEY:			0000933974
		STANDARD INDUSTRIAL CLASSIFICATION:	SPECIAL INDUSTRY MACHINERY, NEC [3559]
		IRS NUMBER:				043040660
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			0930

	BUSINESS ADDRESS:	
		STREET 1:		15 ELIZABETH DRIVE
		CITY:			CHELMSFORD
		STATE:			MA
		ZIP:			01824
		BUSINESS PHONE:		(978) 262-2400

	MAIL ADDRESS:	
		STREET 1:		15 ELIZABETH DRIVE
		CITY:			CHELMSFORD
		STATE:			MA
		ZIP:			01824

	FORMER COMPANY:	
		FORMER CONFORMED NAME:	BROOKS-PRI AUTOMATION INC
		DATE OF NAME CHANGE:	20020514

	FORMER COMPANY:	
		FORMER CONFORMED NAME:	BROOKS AUTOMATION INC
		DATE OF NAME CHANGE:	19941215

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			GRILK THOMAS S
		CENTRAL INDEX KEY:			0001234454

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-25434
		FILM NUMBER:		071321809

	BUSINESS ADDRESS:	
		STREET 1:		15 ELIZABETH DRIVE
		CITY:			CHELMSFORD
		STATE:			MA
		ZIP:			01824
		BUSINESS PHONE:		9782622400
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>doc4.xml
<DESCRIPTION>FORM 4 SUBMISSION
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2007-12-20</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0000933974</issuerCik>
        <issuerName>BROOKS AUTOMATION INC</issuerName>
        <issuerTradingSymbol>BRKS</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001234454</rptOwnerCik>
            <rptOwnerName>GRILK THOMAS S</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O BROOKS AUTOMATION, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>15 ELIZABETH DRIVE</rptOwnerStreet2>
            <rptOwnerCity>CHELMSFORD</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>01824</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Sr. VP, General Counsel</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2007-12-20</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>F</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>475</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>12.49</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>47471</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">Forfeiture of shares by the reporting person to satisfy the reporting person's obligations with respect to withholding taxes in connection with the vesting on December 20, 2007 of 1,500 shares of restricted stock held by the reporting person.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Thomas S. Grilk</signatureName>
        <signatureDate>2007-12-21</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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