<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0201</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2003-10-01</periodOfReport>

    <noSecuritiesOwned>1</noSecuritiesOwned>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001041888</rptOwnerCik>
            <rptOwnerName>ALLEN A CLINTON</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>15 ELIZABETH DRIVE</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>CHELMSFORD</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>01824</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
            <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <ownerSignature>
        <signatureName>By: Lynda M. Avallone  For: A. Clinton Allen</signatureName>
        <signatureDate>2003-10-03</signatureDate>
    </ownerSignature>

</ownershipDocument>

