UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, DC 20549





Form 10-K/A

ANNUAL REPORT

PURSUANT TO SECTIONS 13 OR 15(d)

OF THE SECURITIES EXCHANGE ACT OF
1934



| ̈ | ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
|- | ------------------------------------------------------------------------------------

For the fiscal year ended December 31, 2012

or



| ̈ | TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
|- | ----------------------------------------------------------------------------------------

For the transition period from                  to

Commission file number
0-29801





INTERMUNE, INC.

(Exact name of registrant as specified in its charter)



|                                                               |  |                                  
|-------------------------------------------------------------- |  | ---------------------------------
|Delaware                                                       |  | 94-3296648                       
|(State or other jurisdiction of
incorporation or organization) |  | (IRS Employer identification No.)

3280 Bayshore Boulevard

Brisbane, CA 94005

(Address of principal executive offices, including
Zip Code)

(415) 466-2200

(Registrants telephone number, including area code)

Securities
registered pursuant to Section 12(b) of the Act:



|                               |  |                                     
|------------------------------ |  | ------------------------------------
|Title of Each Class            |  | Name of Exchange on which
Registered
|Common Stock, $0.001 par value |  | The NASDAQ Stock Market LLC.        

Securities registered pursuant to Section 12(g) of the Act: None





Indicate by check mark if the registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities
Act. Yes þ No  ̈

Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Securities Exchange Act of 1934. Yes  ̈ No þ

Indicate by check
mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to
file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes þ No  ̈

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every
Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files). Yes þ No  ̈

Indicate by check
mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K is not contained herein, and will not be contained, to the best of registrants knowledge, in definitive proxy or information statements incorporated by
reference in Part III of this Form 10-K or any amendment to this Form 10-K.  ̈

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer or a smaller reporting company. See the definitions of large accelerated
filer, accelerated filer and smaller reporting company in Rule 12b-2 of the Exchange Act. (Check one):



|                        |  |                                                  |  |                           |  |  
|----------------------- |  | ------------------------------------------------ |  | ------------------------- |  | -
|Large accelerated filer |  | þ                                                |  | Accelerated filer         |  |  ̈
|                        |  |                                                  | 
|Non-accelerated filer   |  |  ̈  (Do not check if a smaller reporting company) |  | Smaller reporting company |  |  ̈

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the
Exchange Act). Yes  ̈ No þ

As of June 29, 2012, the last business day of the registrants second fiscal quarter, the aggregate market value (based upon the closing sales price of such stock as reported on The NASDAQ
Global Select Market) of the voting and non-voting stock held by non-affiliates of the registrant was $778,641,828, which excludes an aggregate of 580,030 shares of the registrants common stock held by affiliates as of such date. Exclusion of
shares held by any person should not be construed to indicate that such person possesses the power, direct or indirect, to direct or cause the direction of the management or policies of the registrant, or that such person is controlled by or under
common control with the registrant. As of January 31, 2013, the number of outstanding shares of the registrants common stock was 81,600,709 shares.

DOCUMENTS INCORPORATED BY REFERENCE

Portions of the registrants
definitive Proxy Statement for the 2013 Annual Meeting of Stockholders to be filed with the Securities and Exchange Commission pursuant to Regulation 14A not later than 120 days after the end of the fiscal year covered by this Form 10-K are
incorporated by reference in Part III, Items 10-14 of this Annual Report on Form 10-K.









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EXPLANATORY NOTE

The registrant is filing this Amendment No. 1 to Annual Report on Form 10-K/A, or this Amendment, to amend the Annual Report on Form
10-K for the fiscal year ended December 31, 2012 (Commission File Number 001-29801), or the Form 10-K, as filed by the registrant with the Securities and Exchange Commission, or the SEC, on March 1, 2013. The purpose of this Amendment is
to amend and restate Item 9A. Controls and Procedures for the purpose of disclosing the conclusions of our Chief Executive Officer and Chief Financial Officer regarding the effectiveness of our disclosure controls and procedures as of
December 31, 2012. In addition, as required by Rule 12b-15 under the Securities Exchange Act of 1934, as amended, new certifications by the registrants principal executive officer and principal financial officer are filed as exhibits to
this Amendment

No other changes have been made to the Form 10-K other than those described above. This Amendment does not
reflect subsequent events occurring after the original filing date of the Form 10-K or modify or update in any way disclosures made in the Form 10-K.

ITEM 9A. CONTROLS AND PROCEDURES

Evaluation of Disclosure Controls and
Procedures. We maintain disclosure controls and procedures, as such term is defined in Rule 13a-15(e) under the Exchange Act, that are designed to ensure that information required to be disclosed by us in reports that we file or
submit under the Exchange Act is recorded, processed, summarized and reported within the time periods specified in SEC rules and forms, and that such information is accumulated and communicated to our management, including our Chief Executive
Officer and Chief Financial Officer, as appropriate to allow timely decisions regarding required disclosure. In designing and evaluating our disclosure controls and procedures, management recognized that disclosure controls and procedures, no matter
how well conceived and operated, can provide only reasonable, not absolute, assurance that the objectives of the disclosure controls and procedures are met. Additionally, in designing disclosure controls and procedures, our management necessarily
was required to apply its judgment in evaluating the cost-benefit relationship of possible disclosure controls and procedures. The design of any disclosure controls and procedures also is based in part upon certain assumptions about the likelihood
of future events, and there can be no assurance that any design will succeed in achieving its stated goals under all potential future conditions.

Based on their evaluation as of the end of the period covered by this Annual Report on Form 10-K, as discussed further below, our Chief Executive Officer and Chief Financial Officer have concluded that
our disclosure controls and procedures were not effective at the reasonable assurance level.

Managements Report on Internal Control
Over Financial Reporting. Our management is responsible for establishing and maintaining adequate internal control over financial reporting as defined in Rule 13a-15(f) of the Exchange Act. Because of its inherent limitations, internal control
over financial reporting may not prevent or detect misstatements. Also, projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree
of compliance with the policies or procedures may deteriorate.

We have identified a control deficiency under ASC 740, accounting for income
taxes, related to an intraperiod tax allocation resulting from our sale of Actimmune on June 19, 2012. Our failure to correctly record this intraperiod tax allocation affected the presentation of income tax expense for the three and six month
periods ended June 30, 2012 and the three and nine month periods ended September 30, 2012. In particular, our Quarterly Reports on Form 10-Q for the quarters ended June 30, 2012 and September 30, 2012 did not correctly present
the intraperiod tax allocation of income tax expense (benefit) from continuing and discontinued operations in accordance with ASC 740. As a result, we have restated our financial statements for these periods. We have also determined to restate our
previous presentation of the comparable financial results for the three and six month periods ended June 30, 2011 and the three and nine months periods ended September 30, 2011 as stated in the Companys Quarterly Reports on Form 10-Q
for the quarters ended June 30, 2012 and September 30, 2012. The resulting restatements are more fully described in Note 19 to the financial statements included in this Form 10-K. The control deficiency relates to a failure to completely
review the tax consequences of complex and infrequent transactions, and we have determined that this matter represented a material weakness in our internal control as of December 31, 2012.

A material weakness is a significant deficiency, as defined in Public Company Accounting Oversight Board Auditing Standard No. 2, or combination of
significant deficiencies, that results in a more than remote likelihood that a material misstatement of a companys annual or interim financial statements would not be prevented or detected by company personnel in the normal course of
performing their assigned functions. Management assessed the effectiveness of our internal control over financial reporting as of December 31,



---

2012. In making this assessment, we used the criteria set forth by the Committee of Sponsoring Organizations of the Treadway Commission in Internal ControlIntegrated Framework. Based on our
assessment using those criteria, management concluded that the design and operating effectiveness of our internal control over financial reporting was not effective as of December 31, 2012 based on the control deficiency over the accounting for
the tax consequences of complex and infrequent transactions described above.

Changes in Internal Control over Financial Reporting.
Under the rules of the Securities and Exchange Commission, internal control over financial reporting is defined as a process designed by, or under the supervision of, an issuers principal executive and principal financial officers,
and effected by the issuers board of directors, management and other personnel, to provide reasonable assurances regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance
with generally accepted accounting principles.

There were no changes to our internal control over financial reporting during our last fiscal
quarter that have materially affected, or are reasonable likely to materially affect, our internal control over financial reporting. However, as a result of the matter that led to the restatement and the related assessment of internal control over
financial reporting, the Company is implementing remediation steps to address the material weakness discussed above and to improve its internal controls over financial reporting.

We have developed a remediation plan to address these deficiencies and implemented this plan in February 2013. The plan includes enhancing our review procedures around the tax consequences of complex and
infrequent transactions. We believe that our remediation plan will strengthen our internal control over financial reporting and should remediate the material weakness we have identified.

Limitations on the Effectiveness of Controls. Our management, including the Chief Executive Officer and Chief Financial Officer, does not expect that our disclosure controls and procedures or our
internal control over financial reporting will prevent all error and all fraud. A control system, no matter how well designed and operated, can provide only reasonable, not absolute, assurance that the objectives of the control system are met.
Because of the inherent limitations in all control systems, no evaluation of controls can provide absolute assurance that all control issues and instances of fraud, if any, within the company have been detected.

Because of its inherent limitations, internal control over financial reporting can provide only reasonable assurance that the objectives of the control
system are met and may not prevent or detect misstatements. In addition, any evaluation of the effectiveness of internal controls over financial reporting in future periods is subject to risk that those internal controls may become inadequate
because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate.



---

EXHIBIT INDEX



|               |  |                                                                                                                                                                                                           |  |                           |  |  |            |  |               |        |  | 
|-------------- |  | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |  | ------------------------- |  |  | ---------- |  | ------------- | ------ |  | 
|Exhibit Number |  | Exhibit Description                                                                                                                                                                                       |  | Incorporated by Reference
|               |  | Form                                                                                                                                                                                                      |  | Date                      |  |  | Number     |  | FiledHerewith
|               |  |                                                                                                                                                                                                           |  |                           | 
|2.1*           |  | Asset Purchase Agreement by and between Registrant and F. Hoffmann-La Roche Ltd and Hoffmann-La Roche Inc., dated as of October 6, 2010                                                                   |  | 8-K                       |  |  | 10/12/2010 |  |               | 2.1    |  | 
|               |  |                                                                                                                                                                                                           |  |                           | 
|2.2(a)         |  | Asset Purchase Agreement by and among Vidara Therapeutics International Limited, Vidara Therapeutics Holdings LLC, Vidara Therapeutics Research Limited and InterMune, dated May 17,
2012.                |  | 10-Q                      |  |  | 08/08/2012 |  |               | 2.1(a) |  | 
|               |  |                                                                                                                                                                                                           |  |                           | 
|2.2(b)         |  | Amendment to Asset Purchase Agreement, dated June 18, 2012, by and among Vidara Therapeutics International Limited, Vidara Therapeutics Holdings LLC, Vidara Therapeutics Research
Limited and InterMune. |  | 10-Q                      |  |  | 08/08/2012 |  |               | 2.1(b) |  | 
|               |  |                                                                                                                                                                                                           |  |                           | 
|3.1            |  | Amended and Restated Certificate of Incorporation of Registrant.                                                                                                                                          |  | S-1/A                     |  |  | 02/18/2000 |  |               | 3.2    |  | 
|               |  |                                                                                                                                                                                                           |  |                           | 
|3.2            |  | Certificate of Ownership and Merger, dated April 26, 2001.                                                                                                                                                |  | 10-Q                      |  |  | 08/03/2001 |  |               | 3.4    |  | 
|               |  |                                                                                                                                                                                                           |  |                           | 
|3.3            |  | Amended and Restated Bylaws of Registrant.                                                                                                                                                                |  | 8-K                       |  |  | 03/24/2010 |  |               | 3.1    |  | 
|               |  |                                                                                                                                                                                                           |  |                           | 
|3.4            |  | Certificate of Amendment of Amended and Restated Certificate of Incorporation of Registrant.                                                                                                              |  | 10-Q                      |  |  | 08/14/2003 |  |               | 3.4    |  | 
|               |  |                                                                                                                                                                                                           |  |                           | 
|3.5            |  | Certificate of Amendment of Amended and Restated Certificate of Incorporation of Registrant.                                                                                                              |  | 10-Q                      |  |  | 08/09/2004 |  |               | 3.5    |  | 
|               |  |                                                                                                                                                                                                           |  |                           | 
|3.6            |  | Certificate of Amendment of Amended and Restated Certificate of Incorporation of Registrant.                                                                                                              |  | S-3                       |  |  | 09/04/2009 |  |               | 3.4    |  | 
|               |  |                                                                                                                                                                                                           |  |                           | 
|3.7            |  | Registrants Certificate of Designation of Series A Junior Participating Preferred Stock.                                                                                                                 |  | 8-K                       |  |  | 07/18/2001 |  |               | 4.3    |  | 
|               |  |                                                                                                                                                                                                           |  |                           | 
|4.1            |  | Reference is made to Exhibits 3.1, 3.2, 3.3, 3.4, 3.5, 3.6 and 3.7.                                                                                                                                       |  |                           |  |  |            |  |               |        |  | 
|               |  |                                                                                                                                                                                                           |  |                           | 
|4.2            |  | Specimen Common Stock Certificate.                                                                                                                                                                        |  | S-1/A                     |  |  | 03/22/2000 |  |               | 4.1    |  | 
|               |  |                                                                                                                                                                                                           |  |                           | 
|4.3            |  | Indenture, dated as of June 24, 2008, between Registrant and The Bank of New York Trust Company, N.A. (including the form of 5.00% convertible senior note due
2015).                                     |  | 8-K                       |  |  | 06/24/2008 |  |               | 4.1    |  | 
|               |  |                                                                                                                                                                                                           |  |                           | 
|4.4            |  | Indenture, dated September 19, 2011, between the Registrant and The Bank of New York Mellon Trust Company, N.A., as Trustee.                                                                              |  | 8-K                       |  |  | 09/19/2011 |  |               | 4.1    |  | 



---

|      |  |                                                                                                                                                                                                                |  |       |  |  |            |  |  |       |  | 
|----- |  | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |  | ----- |  |  | ---------- |  |  | ----- |  | 
|      |  |                                                                                                                                                                                                                |  |       | 
|4.5   |  | First Supplemental Indenture, dated September 19, 2011, between the Registrant and The Bank of New York Mellon Trust Company, N.A., as Trustee (including the form of 2.50%
convertible senior note due 2018). |  | 8-K   |  |  | 09/19/2011 |  |  | 4.2   |  | 
|      |  |                                                                                                                                                                                                                |  |       | 
|4.6   |  | Second Supplemental Indenture, dated January 22, 2013, between InterMune, Inc. and The Bank of New York Mellon Trust Company, N.A., as Trustee (including the form of 2.50%
convertible senior note due 2017). |  | 8-K   |  |  | 01/22/2013 |  |  | 4.2   |  | 
|      |  |                                                                                                                                                                                                                |  |       | 
|10.1+ |  | Form of Indemnity Agreement.                                                                                                                                                                                   |  | S-1   |  |  | 02/02/2000 |  |  | 10.1  |  | 
|      |  |                                                                                                                                                                                                                |  |       | 
|10.2+ |  | 1999 Equity Incentive Plan and related documents.                                                                                                                                                              |  | S-1/A |  |  | 02/18/2000 |  |  | 10.2  |  | 
|      |  |                                                                                                                                                                                                                |  |       | 
|10.3+ |  | Amended and Restated 2000 Equity Incentive Plan and related documents.                                                                                                                                         |  | 8-K   |  |  | 06/08/2012 |  |  | 10.1  |  | 
|      |  |                                                                                                                                                                                                                |  |       | 
|10.4+ |  | Amended and Restated 2000 Employee Stock Purchase Plan and related documents.                                                                                                                                  |  | 10-K  |  |  | 03/14/2008 |  |  | 10.4  |  | 
|      |  |                                                                                                                                                                                                                |  |       | 
|10.5+ |  | Amended and Restated 2000 Non-Employee Directors Stock Option Plan and related documents.                                                                                                                     |  | 10-K  |  |  | 03/14/2008 |  |  | 10.5  |  | 
|      |  |                                                                                                                                                                                                                |  |       | 
|10.6+ |  | Form of Change of Control Provisions for Officers.                                                                                                                                                             |  | 10-Q  |  |  | 05/11/2000 |  |  | 10.20 |  | 
|      |  |                                                                                                                                                                                                                |  |       | 
|10.7  |  | Form of Common Stock Purchase Agreement, dated August 11, 2000, between the Company and Investors.                                                                                                             |  | 8-K   |  |  | 08/23/2000 |  |  | 99.1  |  | 
|      |  |                                                                                                                                                                                                                |  |       | 
|10.8a |  | Lease Agreement, dated December 18, 2000, between Registrant and GAL-BRISBANE, L.P.                                                                                                                            |  | 10-K  |  |  | 03/29/2001 |  |  | 10.31 |  | 
|      |  |                                                                                                                                                                                                                |  |       | 
|10.8b |  | First Amendment to Brisbane Technology Park Lease, effective as of December 18, 2000, between Registrant and GAL-BRISBANE, L.P.                                                                                |  | 10-K  |  |  | 03/29/2001 |  |  | 10.32 |  | 
|      |  |                                                                                                                                                                                                                |  |       | 
|10.8c |  | Second Amendment dated May 3, 2006 to Brisbane Technology Park Lease, effective as of December 18, 2000, between Registrant and BMR-BAYSHORE BOULEVARD LLC (successor-in-interest to
GAL-BRISBANE, L.P.)       |  | 10-Q  |  |  | 11/08/2010 |  |  | 10.1  |  | 
|      |  |                                                                                                                                                                                                                |  |       | 
|10.8d |  | Third Amendment dated August 23, 2006 to Brisbane Technology Park Lease, effective as of December 18, 2000, between Registrant and BMR-BAYSHORE BOULEVARD LLC (successor-in-interest
to GAL-BRISBANE, L.P.)    |  | 10-Q  |  |  | 11/08/2010 |  |  | 10.2  |  | 
|      |  |                                                                                                                                                                                                                |  |       | 
|10.8e |  | Fourth Amendment dated July 16, 2010 to Brisbane Technology Park Lease, effective as of December 18, 2000, between Registrant and BMR-BAYSHORE BOULEVARD LLC (successor-in-interest
to GAL-BRISBANE, L.P.)     |  | 10-Q  |  |  | 11/08/2010 |  |  | 10.3  |  | 



---

|        |  |                                                                                                                                                                                                |  |      |  |  |            |  |  |        |  | 
|------- |  | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |  | ---- |  |  | ---------- |  |  | ------ |  | 
|        |  |                                                                                                                                                                                                |  |      | 
|10.9+   |  | Employment Offer Letter, dated September 24, 2003, between Registrant and Daniel G. Welch.                                                                                                     |  | 10-Q |  |  | 11/13/2003 |  |  | 10.65  |  | 
|        |  |                                                                                                                                                                                                |  |      | 
|10.10   |  | Employment offer letter, dated February 6, 2012, by and between Registrant and Jonathan A. Leff, M.D.                                                                                          |  | 8-K  |  |  | 02/09/2012 |  |  | 10.1   |  | 
|        |  |                                                                                                                                                                                                |  |      | 
|10.11a  |  | Amended and Restated Standstill Agreement, dated October 29, 2004, among Registrant, Warburg Pincus & Co. and certain affiliates of Warburg Pincus &
Co.                                       |  | 8-K  |  |  | 11/04/2004 |  |  | 10.79  |  | 
|        |  |                                                                                                                                                                                                |  |      | 
|10.11b  |  | Amendment, dated January 19, 2010, to Amended and Restated Standstill Agreement, dated October 29, 2004, among Registrant, Warburg Pincus & Co. and certain affiliates
of Warburg Pincus & Co. |  | 8-K  |  |  | 01/19/2010 |  |  | 10.1   |  | 
|        |  |                                                                                                                                                                                                |  |      | 
|10.12   |  | Registration Rights Agreement, dated October 29, 2004, among Registrant, Warburg Pincus & Co. and certain affiliates of Warburg Pincus & Co.                                                   |  | 8-K  |  |  | 11/04/2004 |  |  | 10.80  |  | 
|        |  |                                                                                                                                                                                                |  |      | 
|10.13a+ |  | Employment Offer Letter Agreement, dated June 13, 2001, between Registrant and Williamson Bradford, M.D., Ph.D.                                                                                |  | 10-K |  |  | 03/16/2005 |  |  | 10.83  |  | 
|        |  |                                                                                                                                                                                                |  |      | 
|10.13b+ |  | Amendment to Offer Letter re Severance Pay and Change in Control, dated July 27, 2004, between Registrant and Williamson Bradford, M.D., Ph.D.                                                 |  | 10-K |  |  | 03/16/2005 |  |  | 10.91  |  | 
|        |  |                                                                                                                                                                                                |  |      | 
|10.14a+ |  | Employment Offer Letter Agreement, dated June 1, 2001, between Registrant and Steven Porter, M.D., Ph.D.                                                                                       |  | 10-K |  |  | 03/16/2005 |  |  | 10.85  |  | 
|        |  |                                                                                                                                                                                                |  |      | 
|10.14b+ |  | Amendment to Offer Letter re Severance Pay and Change in Control, dated July 26, 2004, between Registrant and Steven Porter, M.D., Ph.D.                                                       |  | 10-K |  |  | 03/16/2005 |  |  | 10.94  |  | 
|        |  |                                                                                                                                                                                                |  |      | 
|10.15+  |  | Employment Offer Letter Agreement, dated August 9, 2004, between Registrant and Robin Steele.                                                                                                  |  | 10-K |  |  | 03/16/2005 |  |  | 10.86  |  | 
|        |  |                                                                                                                                                                                                |  |      | 
|10.16+  |  | Employment offer letter, dated January 28, 2013, by and between Registrant and Sean P. Nolan                                                                                                   |  | 10-K |  |  | 03/01/2013 |  |  | 10.16  |  | 
|        |  |                                                                                                                                                                                                |  |      | 
|10.17*  |  | Asset Purchase Agreement dated December 23, 2005, between Registrant and Targanta Therapeutics Corporation.                                                                                    |  | 10-K |  |  | 03/13/2006 |  |  | 10.103 |  | 
|        |  |                                                                                                                                                                                                |  |      | 
|10.18+  |  | Employment Offer Letter Agreement, dated July 26, 2006, between Registrant and John C. Hodgman.                                                                                                |  | 10-K |  |  | 03/09/2011 |  |  | 10.33  |  | 
|        |  |                                                                                                                                                                                                |  |      | 
|10.19*  |  | Asset Purchase Agreement, dated November 19, 2007, among Registrant, Marnac, Inc., and Dr. Solomon B. Margolin.                                                                                |  | 10-K |  |  | 03/14/2008 |  |  | 10.59  |  | 
|        |  |                                                                                                                                                                                                |  |      | 
|10.20*  |  | Asset Purchase Agreement, dated November 21, 2007, among Registrant, KDL GmbH, and Dr. Shitotomo Yamauchi.                                                                                     |  | 10-K |  |  | 03/14/2008 |  |  | 10.60  |  | 



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|         |  |                                                                                                                                                                               |  |      |  |  |            |  |  |          |  |  |   | 
|-------- |  | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |  | ---- |  |  | ---------- |  |  | -------- |  |  | - | 
|         |  |                                                                                                                                                                               |  |      | 
|10.21*   |  | API Supply Agreement dated December 17, 2008 among Registrant, on the one hand, and Signa S.A. de C.V., ACIC Fine Chemicals Inc., and ACIC Europe Limited, on the other
hand. |  | 10-K |  |  | 03/16/2009 |  |  | 10.72    |  |  |   | 
|         |  |                                                                                                                                                                               |  |      | 
|10.22*   |  | Commercial Manufacturing Agreement, dated September 10, 2009, by and between Registrant and Catalent Pharma Solutions, LLC.                                                   |  | 10-K |  |  | 03/15/2010 |  |  | 10.75    |  |  |   | 
|         |  |                                                                                                                                                                               |  |      | 
|10.23a+  |  | Employment Offer Letter Agreement, dated October 30, 2009, between Registrant and Giacomo di Nepi.                                                                            |  | 10-K |  |  | 03/09/2011 |  |  | 10.46(a) |  |  |   | 
|         |  |                                                                                                                                                                               |  |      | 
|10.23b+  |  | Employment Letter Arrangement, dated December 28, 2010, between Registrant and Giacomo di Nepi.                                                                               |  | 10-K |  |  | 03/09/2011 |  |  | 10.46(b) |  |  |   | 
|         |  |                                                                                                                                                                               |  |      | 
|10.23c+  |  | Employment Contract, dated December 28, 2010, between InterMune Schweiz AG and Giacomo di Nepi.                                                                               |  | 10-K |  |  | 03/09/2011 |  |  | 10.46(c) |  |  |   | 
|         |  |                                                                                                                                                                               |  |      | 
|21.1     |  | List of Subsidiaries.                                                                                                                                                         |  | 10-K |  |  | 03/01/2013 |  |  | 21.1     |  |  |   | 
|         |  |                                                                                                                                                                               |  |      | 
|23.1     |  | Consent of Independent Registered Public Accounting Firm.                                                                                                                     |  | 10-K |  |  | 03/01/2013 |  |  | 23.1     |  |  |   | 
|         |  |                                                                                                                                                                               |  |      | 
|24.1     |  | Power of Attorney (included on the signature pages hereto)                                                                                                                    |  | 10-K |  |  | 03/01/2013 |  |  | 24.1     |  |  |   | 
|         |  |                                                                                                                                                                               |  |      | 
|31.1     |  | Certification required by Rule 13a-14(a) or Rule 15d-14(a).                                                                                                                   |  |      |  |  |            |  |  |          |  |  | X | 
|         |  |                                                                                                                                                                               |  |      | 
|31.2     |  | Certification required by Rule 13a-14(a) or Rule 15d-14(a).                                                                                                                   |  |      |  |  |            |  |  |          |  |  | X | 
|         |  |                                                                                                                                                                               |  |      | 
|32.1    |  | Certification required by Rule 13a-14(b) or Rule 15d-14(b) and Section 1350 of Chapter 63 of Title 18 of the United States Code (18 U.S.C.
§1350).                            |  | 10-K |  |  | 03/01/2013 |  |  | 32.1     |  |  |   | 
|         |  |                                                                                                                                                                               |  |      | 
|101.INS# |  | XBRL Instance Document                                                                                                                                                        |  | 10-K |  |  | 03/01/2013 |  |  | 101.INS  |  |  |   | 
|         |  |                                                                                                                                                                               |  |      | 
|101.SCH# |  | XBRL Taxonomy Extension Scheme Document                                                                                                                                       |  | 10-K |  |  | 03/01/2013 |  |  | 101.SCH  |  |  |   | 
|         |  |                                                                                                                                                                               |  |      | 
|101.CAL# |  | XBRL Taxonomy Extension Calculation Linkbase Document                                                                                                                         |  | 10-K |  |  | 03/01/2013 |  |  | 101.CAL  |  |  |   | 
|         |  |                                                                                                                                                                               |  |      | 
|101.DEF# |  | XBRL Taxonomy Extension Definition Linkbase Document                                                                                                                          |  | 10-K |  |  | 03/01/2013 |  |  | 101.DEF  |  |  |   | 
|         |  |                                                                                                                                                                               |  |      | 
|101.LAB# |  | XBRL Taxonomy Extension Label Linkbase Document                                                                                                                               |  | 10-K |  |  | 03/01/2013 |  |  | 101.LAB  |  |  |   | 
|         |  |                                                                                                                                                                               |  |      | 
|101.PRE# |  | XBRL Taxonomy Extension Presentation Linkbase Document                                                                                                                        |  | 10-K |  |  | 03/01/2013 |  |  | 101.PRE  |  |  |   | 



|* | Confidential treatment has been granted with respect to certain portions of this exhibit. Omitted portions have been filed separately with the Securities and Exchange
Commission.
|- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



|+ | Management contract or compensation plan or arrangement.
|- | --------------------------------------------------------



| | This certification accompanies the Annual Report pursuant to Section 906 of the Sarbanes-Oxley Act of 2002 and shall not be deemed filed by the
Registrant for purposes of Section 18 of the Securities Exchange Act of 1934, as amended.
|- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



|# | Pursuant to Rule 406T of Regulation S-T, these interactive data files are deemed and filed or part of a registration statement or prospectus for purposes of Sections 11
or 12 of the Securities Act of 1933, as amended, or Section 18 of the Securities Exchange Act of 1934, as amended, and otherwise are not subject to liability under those sections.
|- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



---

SIGNATURES

Pursuant to the requirements of Section 13 or 15(d) of the Securities Act of 1934, the registrant has duly caused this Report to be signed on its behalf by the undersigned, thereunto duly authorized.



INTERMUNE, INC.By:

/S/ JOHN C. HODGMANJohn C. Hodgman Executive Vice President of Finance Administration and Chief Financial Officer


Dated: July 5, 2013