UNITED STATES

SECURITIES AND EXCHANGE

 COMMISSION

Washington, D.C. 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No. 2)*

IntraLinks Holdings, Inc.

 (Name of Issuer)

Common Stock, $0.001 par value per share

(Title of Class of Securities)

46118H104

(CUSIP Number)

Michael R. Murphy

Discovery Group I, LLC

191 North Wacker Drive

Suite 1685

Chicago, Illinois 60606

Telephone Number: (312) 265-9600

(Name, Address and Telephone Number of Person

Authorized to Receive Notices and Communications)

September 25, 2012

(Date of Event which Requires Filing of this Statement)

If the filing person has previously filed a statement on Schedule 13G to report the acquisition that is the subject of this Schedule 13D, and is filing this schedule because of §§240.13d-1(e), 240.13d-1(f) or 240.13d-1(g), check the following box. o

Note: Schedules filed in paper format shall include a signed original and five copies of the schedule, including all exhibits. See §240.13d-7 for other parties to whom copies are to be sent.

*The remainder of this cover page shall be filled out for a reporting person's initial filing on this form with respect to the subject class of securities, and for any subsequent amendment containing information which would alter disclosures provided in a prior cover page.

The information required on the remainder of this cover page shall not be deemed to be "filed" for the purpose of Section 18 of the Securities Exchange Act of 1934 ("Act") or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes).

CUSIP No. 46118H104
	1.	Names of Reporting Persons. Discovery Equity Partners, L.P.
	2.	Check the Appropriate Box if a Member of a Group (See Instructions)
		(a)			o
		(b)			o
	3.	SEC Use Only
	4.	Source of Funds (See Instructions) WC
	5.	Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e)     o
	6.	Citizenship or Place of Organization Illinois
Number of Shares Beneficially Owned by Each Reporting Person With			7.	Sole Voting Power None.
			8.	Shared Voting Power 2,727,188
			9.	Sole Dispositive Power None.
			10.	Shared Dispositive Power 2,727,188
	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 2,727,188
	12.	Check if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions)   o
	13.	Percent of Class Represented by Amount in Row (11) 4.9%
	14.	Type of Reporting Person (See Instructions) PN

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CUSIP No.  46118H104
	1.	Names of Reporting Persons. Discovery Group I, LLC
	2.	Check the Appropriate Box if a Member of a Group (See Instructions)
		(a)			o
		(b)			o
	3.	SEC Use Only
	4.	Source of Funds (See Instructions) AF
	5.	Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e)     o
	6.	Citizenship or Place of Organization Delaware
Number of Shares Beneficially Owned by Each Reporting Person With			7.	Sole Voting Power None.
			8.	Shared Voting Power 3,151,707
			9.	Sole Dispositive Power None.
			10.	Shared Dispositive Power 3,151,707
	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 3,151,707
	12.	Check if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions)   o
	13.	Percent of Class Represented by Amount in Row (11) 5.7%
	14.	Type of Reporting Person (See Instructions) IA

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CUSIP No.  46118H104
	1.	Names of Reporting Persons. Daniel J. Donoghue
	2.	Check the Appropriate Box if a Member of a Group (See Instructions)
		(a)			o
		(b)			o
	3.	SEC Use Only
	4.	Source of Funds (See Instructions) AF
	5.	Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e)     o
	6.	Citizenship or Place of Organization United States of America
Number of Shares Beneficially Owned by Each Reporting Person With			7.	Sole Voting Power None.
			8.	Shared Voting Power 3,151,707
			9.	Sole Dispositive Power None.
			10.	Shared Dispositive Power 3,151,707
	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 3,151,707
	12.	Check if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions)   o
	13.	Percent of Class Represented by Amount in Row (11) 5.7%
	14.	Type of Reporting Person (See Instructions) IN

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CUSIP No.  46118H104
	1.	Names of Reporting Persons. Michael R. Murphy
	2.	Check the Appropriate Box if a Member of a Group (See Instructions)
		(a)			o
		(b)			o
	3.	SEC Use Only
	4.	Source of Funds (See Instructions) AF
	5.	Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e)     o
	6.	Citizenship or Place of Organization United States of America
Number of Shares Beneficially Owned by Each Reporting Person With			7.	Sole Voting Power None.
			8.	Shared Voting Power 3,151,707
			9.	Sole Dispositive Power None.
			10.	Shared Dispositive Power 3,151,707
	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 3,151,707
	12.	Check if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions)   o
	13.	Percent of Class Represented by Amount in Row (11) 5.7%
	14.	Type of Reporting Person (See Instructions) IN

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Item 1.		Security and Issuer
		This Amendment No. 2 to Schedule 13D (“Amendment No. 2”) relates to the Common Stock, $0.001 par value per share (the “Common Stock”), of IntraLinks Holdings, Inc., a Delaware corporation (the “Company”), which has its principal executive offices at 150 East 42nd Street, 8th Floor, New York, New York 10017.  This Amendment No. 2 amends and supplements, as set forth below, the information contained in items 1, 3, 5 and 6 of the Schedule 13D filed by the Reporting Persons with respect to the Company on December 2, 2011 (as so amended, the “Schedule 13D”).  All capitalized terms used herein but not defined herein have the meanings set forth in the Schedule 13D.  Except as amended by this Amendment No. 2, all information contained in the Schedule 13D is, after reasonable inquiry and to the best of the Reporting Persons’ knowledge and belief, complete and correct as of the date of this Amendment No. 2.
Item 3.		Source and Amount of Funds or Other Consideration
		Item 3 of the Schedule 13D is hereby amended to read in its entirety as follows: The total purchase price for the 3,151,707 shares of Common Stock beneficially owned by Discovery Group and Messrs. Donoghue and Murphy as of September 26, 2012 was approximately $18,245,234 and the total purchase price for the 2,727,188 shares of Common Stock beneficially owned by Discover Equity Partners was approximately $15,920,755.  The source of such funds was the assets of Discovery Equity Partners and another private investment partnership (collectively, the “Partnerships”) over which Discovery Group exercises discretionary investment management authority, and proceeds of margin loans under margin loan facilities maintained in the ordinary course of business by the Partnerships with a broker on customary terms and conditions.  The Partnerships are the legal owner of all of the Common Stock beneficially owned by Discovery Group and Messrs. Donoghue and Murphy.
Item 5.		Interest in Securities of the Issuer
		Item 5 of the Schedule 13D is hereby amended to read in its entirety as follows: The information concerning percentages of ownership set forth below is based on 55,066,676 shares of Common Stock reported outstanding as of August 7, 2012 in the Company’s most recent Quarterly Report on Form 10-Q, for the quarter ended June 30, 2012. Discovery Equity Partners beneficially owns 2,727,188 shares of Common Stock as of September 25, 2012, which represents 4.9% of the outstanding Common Stock. Discovery Group beneficially owns 3,151,707 shares of Common Stock as of September 25, 2012, which represents 5.7% of the outstanding Common Stock. Mr. Donoghue beneficially owns 3,151,707 shares of Common Stock as of September 25, 2012, which represents 5.7% of the outstanding Common Stock. Mr. Murphy beneficially owns 3,151,707 shares of Common Stock as of September 25, 2012, which represents 5.7% of the outstanding Common Stock. Discovery Group is the sole general partner of Discovery Equity Partners and has sole discretionary investment authority with respect to the other Partnership’s investment in the Common Stock.  Messrs. Donoghue and Murphy are the sole managing members of Discovery Group.  As a consequence, Discovery Group and Messrs. Donoghue and Murphy may be deemed to share beneficial ownership of all of the shares of Common Stock owned by both of the Partnerships, while Discovery Equity Partners shares beneficial ownership with Discovery Group and Messrs. Donoghue and Murphy of only the shares of Common Stock owned by it.
		The transactions in Common Stock effected by the Reporting Persons during the past 60 days are set out in Exhibit 1 hereto. Discovery Equity Partners ceased to be the beneficial owner of more than five percent of the Common Stock on September 25, 2012. No person other than the Partnerships is known to any Reporting Person to have the right to receive or the power to direct the receipt of dividends from, or the proceeds from the sale of, any of the shares of Common Stock reported herein.
Item 6.		Contracts, Arrangements, Understandings or Relationships with Respect to Securities of the Issuer
		Item 6 of the Schedule 13D is hereby amended to read in its entirety as follows: There are no contracts, arrangements, understandings or relationships (legal or otherwise) between or among any of the Reporting Persons and any other person with respect to any securities of the Company other than the governing documents of Discovery Group and the Partnerships, the margin loan facilities referred to under Item 3 of the Schedule 13D, the Joint Filing Agreements of the Reporting Persons with respect to the Schedule 13D that were included as exhibits thereto, the Joint Filing Agreement of the Reporting Persons with respect to this Amendment No. 2 included as Exhibit 2 to this Amendment No. 2, and the Powers of Attorney granted by Messrs Donoghue and Murphy with respect to reports under Section 13 of the Securities Exchange Act of 1934, as amended, which Powers of Attorney are included as Exhibit 3 and Exhibit 4, respectively, to this Amendment No. 2.
Item 7.	Material to Be Filed as Exhibits
	Exhibit 1:  List of transactions effected by the Reporting Persons in the Company’s Common Stock during the 60-day period preceding this filing.
	Exhibit 2:  Joint Filing Agreement dated as of September 27, 2012, by and among Discovery Equity Partners; Discovery Group; Daniel J. Donoghue; and Michael R. Murphy.
	Exhibit 3:  Power of Attorney of Daniel J. Donoghue, dated as of April 28, 2008.
	Exhibit 4:  Power of Attorney of Michael R. Murphy, dated as of April 28, 2008.

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Signature

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

September 27, 2012

Date

DISCOVERY GROUP I, LLC,

for itself and as general partner of

DISCOVERY EQUITY PARTNERS, L.P.

By:  Michael R. Murphy*

Signature

Michael R. Murphy, Managing Member

Name/Title

Daniel J. Donoghue*

Signature

Daniel J. Donoghue

Name/Title

Michael R. Murphy*

Signature

Michael R. Murphy

Name/Title

*By: /s/ Mark Buckley

Mark Buckley

Attorney-in-Fact for Daniel J. Donoghue

Attorney-in-Fact for Michael R. Murphy

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Exhibit Index

Exhibit 1	List of transactions effected by the Reporting Persons in the Company’s Common Stock during the 60-day period preceding this filing.
Exhibit 2	Joint Filing Agreement dated as of September 27, 2012, by and among Discovery Equity Partners; Discovery Group; Daniel J. Donoghue; and Michael R. Murphy.
Exhibit 3	Power of Attorney of Daniel J. Donoghue, dated as of April 28, 2008.
Exhibit 4	Power of Attorney of Michael R. Murphy, dated as of April 28, 2008.

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