UNITED STATES
SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549



---

FORM 10-K/A



Amendment No. 1



---

(Mark One)

| | x | 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



| | o | 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 001-35622

---



Albany Molecular Research, Inc.

(Exact name of registrant as specified in
its charter)



|Delaware                                 |  | 14-1742717         
|---------------------------------------- |  | -------------------
|(State or other jurisdiction of          |  | (I.R.S. Employer   
|incorporation or organization)           |  | Identification No.)
|26 Corporate Circle                      |  |                    
|Albany, New York                         |  | 12203              
|(Address of principal executive offices) |  | (zip code)         



(518) 512-2000

(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, par value $.01 per share |  | The NASDAQ Stock Market LLC         
|Preferred Stock Purchase Rights        |  |                                     



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

None

(Title of Each Class)



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



Indicate
by check mark if the registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Act.
Yeso   No  x



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.  Yesx    No  o



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). Yesx    No  o



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.x



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 definitions of “large accelerated filer”, “accelerated filer” and “smaller reporting
company” in 12b-2 of the Exchange Act



|oLarge accelerated filer |  | xAccelerated filer |  | oNon-accelerated filer |  | oSmaller reporting company
|------------------------ |  | ------------------ |  | ---------------------- |  | --------------------------



Indicate
by checkmark whether the registrant is a shell company (as defined in Rule 12b-2 of the Act). Yeso    No  x



The aggregate market value of the Registrant’s
Common Stock held by non-affiliates of the Registrant on June 30, 2012 was approximately $58 million based upon the closing
price per share of the Registrant’s Common Stock as reported on the Nasdaq Global Market on June 30, 2012. Shares of
Common Stock held by each officer and director and by each person who owns 10% or more of the outstanding Common Stock have been
excluded in that such persons may be deemed to be affiliates. This determination of affiliate status is not necessarily a conclusive
determination for other purposes. As of February 28, 2013, there were 31,337,423 outstanding shares of the Registrant’s
Common Stock, excluding treasury shares of 5,411,372.



























DOCUMENTS INCORPORATED BY REFERENCE



The information required
pursuant to Part III of this report is incorporated by reference from the Company’s definitive proxy statement, relating
to the annual meeting of stockholders held on June 5, 2013, pursuant to Regulation 14A, filed with the Securities and Exchange
Commission.


















EXPLANATORY
NOTE





Albany Molecular Research, Inc. (the “Company”)
is filing this Amendment No. 1 (this “Amendment”) to its Annual Report on Form 10-K for the fiscal year ended December
31, 2012 (the “Form 10-K”), originally filed on March 18, 2013, as an exhibit-only filing in response to comments received
from the Securities and Exchange Commission regarding a request for confidential treatment of certain portions of Exhibit 10.15
originally filed with the Form 10-K. This Amendment is being filed solely to re-file Exhibit 10.15. In addition, as required by
Rule 12b-15 under the Securities Exchange Act of 1934, as amended, new certifications by our principal executive officer and principal
financial officer are filed as exhibits to this Amendment.



This Amendment is limited in scope to the
items identified above and should be read in conjunction with the Form 10-K. This Amendment does not reflect events occurring after
the filing of the Form 10-K and no revisions are being made to the Company’s financial statements pursuant to this Amendment.
Other than the filing of the information identified above, this Amendment does not modify or update the disclosure in the Form
10-K in any way.











ITEM 15. EXHIBITS AND FINANCIAL STATEMENT
SCHEDULES



EXHIBIT INDEX



| | Exhibit

Number | Description
| | --------------- | -----------



| | 10.15 | Supply Agreement, effective as of January 1, 2012, between AMRI Rensselaer, Inc. and GE Healthcare AS (filed herein with certain
information omitted pursuant to a request for confidential treatment and filed separately with the Securities and Exchange Commission).
| | ----- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| | 32.1 | Certification of principal executive officer pursuant to Rule 13a-14(a) and 15d-14(a) of the Securities Exchange Act of 1934,
as amended (filed herein).
| | ---- | --------------------------------------------------------------------------------------------------------------------------------------------------------



| | 32.2 | Certification of principal financial officer pursuant to Rule 13a-14(a) and 15d-14(a) of the Securities Exchange Act of 1934,
as amended (filed herein).
| | ---- | --------------------------------------------------------------------------------------------------------------------------------------------------------











SIGNATURES



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



|Dated: August 27, 2013 | Albany Molecular Research, Inc.
|---------------------- | -------------------------------
|                       | By:                            
|                       |                                
|                       |                                



Pursuant to the requirements of the Securities
Exchange Act of 1934, this report has been signed below by the following persons on behalf of the registrant and in the capacities
and on the dates indicated.



|                            | Signature |                                                       |  |                 | Title |  |  |  | Date | 
|--------------------------- | --------- | ----------------------------------------------------- |  | --------------- | ----- |  |  |  | ---- | 
|/s/ Thomas E. D’Ambra       |           | President, Chief Executive Officer and Director       |  | August 27, 2013
|Thomas E. D’Ambra, Ph.D.    |           | (Principal Executive Officer)                         |  |                
|/s/ Michael M. Nolan        |           | Vice President, Chief Financial Officer and Treasurer |  | August 27, 2013
|Michael M. Nolan            |           | (Principal Financial and Accounting Officer)          |  |                
|/s/ Veronica G.H. Jordan    |           | Director                                              |  | August 27, 2013
|Veronica G.H. Jordan, Ph.D. |           |                                                       |  |                
|/s/ Gabriel Leung           |           | Director                                              |  | August 27, 2013
|Gabriel Leung               |           |                                                       |  |                
|/s/ William Marth           |           | Chairman of the Board                                 |  | August 27, 2013
|William Marth               |           |                                                       |  |                
|/s/ Kevin O’Connor          |           | Director                                              |  | August 27, 2013
|Kevin O’Connor              |           |                                                       |  |                
|/s/ Arthur J. Roth          |           | Director                                              |  | August 27, 2013
|Arthur J. Roth              |           |                                                       |  |                
|/s/ Una S. Ryan             |           | Director                                              |  | August 27, 2013
|Una S. Ryan, Ph.D., O.B.E.  |           |                                                       |  |