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Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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MIC-Info: RSA-MD5,RSA,
 APTkoqfsaTSx02vM0KyiGDhXHJokVEw3QxAi0eqEWpVNmoinoQ5Lg5FrmRIb6l7l
 O5/ap23hGxhG9haqib0AjQ==

<SEC-DOCUMENT>0001231977-04-000002.txt : 20040209
<SEC-HEADER>0001231977-04-000002.hdr.sgml : 20040209
<ACCEPTANCE-DATETIME>20040209172839
ACCESSION NUMBER:		0001231977-04-000002
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20031231
FILED AS OF DATE:		20040209

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			ALEXION PHARMACEUTICALS INC
		CENTRAL INDEX KEY:			0000899866
		STANDARD INDUSTRIAL CLASSIFICATION:	PHARMACEUTICAL PREPARATIONS [2834]
		IRS NUMBER:				133648318
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			0731

	BUSINESS ADDRESS:	
		STREET 1:		352 KNOTTER DRIVE
		CITY:			CHESHIRE
		STATE:			CT
		ZIP:			06511
		BUSINESS PHONE:		2037761790

	MAIL ADDRESS:	
		STREET 1:		352 KNOTTER DRIVE
		CITY:			CHESHIRE
		STATE:			CT
		ZIP:			06511

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			SQUINTO STEPHEN P
		CENTRAL INDEX KEY:			0001231954

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-27756
		FILM NUMBER:		04578944

	MAIL ADDRESS:	
		STREET 1:		C/O ALEXION PHARMACEUTICALS INC
		STREET 2:		352 KNOTTER DRIVE
		CITY:			CHESHIRE
		STATE:			CT
		ZIP:			06410
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>primary_doc.xml
<DESCRIPTION>PRIMARY DOCUMENT
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0201</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2003-12-31</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0000899866</issuerCik>
        <issuerName>ALEXION PHARMACEUTICALS INC</issuerName>
        <issuerTradingSymbol>alxn</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001231954</rptOwnerCik>
            <rptOwnerName>SQUINTO STEPHEN P</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O ALEXION PHARMACEUTICALS INC</rptOwnerStreet1>
            <rptOwnerStreet2>352 KNOTTER DRIVE</rptOwnerStreet2>
            <rptOwnerCity>CHESHIRE</rptOwnerCity>
            <rptOwnerState>CT</rptOwnerState>
            <rptOwnerZipCode>06410</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Exec VP, Head of Research</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock, par value $.0001</value>
            </securityTitle>
            <transactionDate>
                <value>2003-12-31</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>J</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>399</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>17.35</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>25476</value>
                    <footnoteId id="F2"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">Required distribution from Long Pond 2000 Charitable Remainder Trust, of which Dr. Squinto and his spouse are trustees and beneficiaries.</footnote>
        <footnote id="F2">Does not include the following shares of Common Stock, as to which Dr. Squinto disclaims beneficial interest: (1) 8,517 shares held by the Long Pond 2000 Charitable Remainder Trust, of which Dr. Squinto and his spouse are the trustees and beneficiaries, and from which Dr. Squinto has received the Common Stock referred to in this Form 4 in satisfaction of the Trust's obligation to pay him 5.7% of its assets for the year 2003; and (2) 1,906 shares, 2,600 shares and 2,600 shares of Common Stock for each of his 3 minor children, respectively.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>Dr. Stephen P. Squinto</signatureName>
        <signatureDate>2004-02-09</signatureDate>
    </ownerSignature>
</ownershipDocument>

</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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