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

    <schemaVersion>X0202</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2005-07-01</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0000902607</rptOwnerCik>
            <rptOwnerName>KHOURY AMIN J</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>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Non-Qualified Stock Option (right to buy)</value>
                <footnoteId id="F1"/>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>14.84</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2005-07-01</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>10000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F3"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2005-10-01</value>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <value>2012-07-01</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>10000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>10000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Grant to reporting person of option to buy the number of shares of Common Stock set forth in Table II, Column 7 under the Brooks Automation, Inc. 2000 Equity Incentive Stock Option Plan.  The reporting person cannot acquire ownership of any such shares until the option price for such shares as set forth in Column 2 hereof has been paid to Brooks Automation, Inc.</footnote>
        <footnote id="F2">The option becomes exercisable in 16 equal quarterly increments beginning on the date set forth in Table II, Column 6.</footnote>
        <footnote id="F3">The reporting person cannot acquire ownership of any such shares until the option price for such shares as set forth in Column 2 hereof has been paid to Brooks Automation, Inc.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>By: Lynda M. Avallone Attorney-in-Fact  For: Amin Khoury</signatureName>
        <signatureDate>2005-07-05</signatureDate>
    </ownerSignature>
</ownershipDocument>
