<SEC-DOCUMENT>0001209191-18-060601.txt : 20181203
<SEC-HEADER>0001209191-18-060601.hdr.sgml : 20181203
<ACCEPTANCE-DATETIME>20181203171553
ACCESSION NUMBER:		0001209191-18-060601
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20181129
FILED AS OF DATE:		20181203
DATE AS OF CHANGE:		20181203

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Joseph Jason
		CENTRAL INDEX KEY:			0001485448

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-25434
		FILM NUMBER:		181214727

	MAIL ADDRESS:	
		STREET 1:		170 TRACER LANE
		CITY:			WALTHAM
		STATE:			MA
		ZIP:			02451

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
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>doc4.xml
<DESCRIPTION>FORM 4 SUBMISSION
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2018-11-29</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001485448</rptOwnerCik>
            <rptOwnerName>Joseph Jason</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>VP, General Counsel, Secretary</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2018-11-29</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>5356</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>94014</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">Grant of restricted stock units to the Reporting Person under the Company's Long Term Incentive Plan. No amount was paid upon grant of the units. The units are subject to time-based vesting and will vest 33-1/3% per year, beginning on November 15, 2019.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Jason W. Joseph</signatureName>
        <signatureDate>2018-12-03</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
