United States

SECURITIES AND EXCHANGE COMMISSION

Washington, DC 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 September 30, 2009

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 No. 001-33322





CMS BANCORP, INC.

(Exact name of registrant as specified in its charter)



|                                                               |  |                                     
|-------------------------------------------------------------- |  | ------------------------------------
|Delaware                                                       |  | 20-8137247                          
|(State or other jurisdiction of
incorporation or organization) |  | (I.R.S. Employer Identification No.)
|                                                               | 
|123 Main Street White Plains, New York                         |  | 10601                               
|(Address of principal executive offices)                       |  | (Zip Code)                          

(914) 422-2700

(Registrants telephone number, including area code)

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



|                                        |  |                                          
|--------------------------------------- |  | -----------------------------------------
|Title of each class                     |  | Name of each exchange on which registered
|Common Stock, par value $0.01 per share |  | Nasdaq Capital Market                    

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

None.

(Title of Class)

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

Indicate by checkmark 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  x    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 (§ 232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such
files).    Yes   ̈    No   ̈

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K (§ 229.405 of this chapter) 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 the definitions of large accelerated filer, accelerated filer and smaller reporting company in Rule
12b-2 of the Exchange Act.



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

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

The aggregate market value of the voting and non-voting common equity held by non-affiliates of the registrant, computed by reference to
the average bid and asked prices of the common stock as of March 31, 2009 was $11.1 million.

As of December 15,
2009, the registrant had 1,862,803 shares of common stock, par value $0.01 per share, outstanding.









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EXPLANATORY NOTE:

This Amendment No. 1 (this Amendment No. 1) to Form 10-K for the fiscal year ended September 30, 2009 is being filed to include the signature of the Chief Financial Officer
(Principal Financial and Accounting Officer), which was inadvertently omitted from the signature page to the Form 10-K filed on December 15, 2009. This Amendment No. 1 is also being filed to identify the Principal Executive Officer,
whose identification was inadvertently omitted from the signature page.

We are also including in this Amendment No. 1 updated Exhibit
Index references and certifications of our principal executive and principal financial officers. This Amendment No. 1 to our Annual Report on Form 10-K as originally filed on December 15, 2009 (the Original Report)
continues to speak as of the date of our Original Report, and we have not updated the disclosures contained in this Amendment No. 1 to reflect any events that occurred subsequent to the filing of the Original Report.



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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.



CMS BANCORP, INC.By:

/S/ JOHN E.
RITACCOJohn E. Ritacco President and Chief Executive Officer


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.



|                                                  |  |                                                                                               |  |                  
|------------------------------------------------- |  | --------------------------------------------------------------------------------------------- |  | -----------------
|Name                                              |  | Title                                                                                         |  | Date             
|                                                  |  |                                                                                              
|/S/ THOMAS G. FERRARA
Thomas G. Ferrara           |  | Chairman of the Board of Directors                                                            |  | December 15, 2009
|                                                  |  |                                                                                              
|/S/ JOHN E. RITACCO
John E. Ritacco               |  | President, Chief Executive Officer and Director(Principal Executive Officer)                  |  | December 15, 2009
|                                                  |  |                                                                                              
|/S/ STEPHEN E. DOWD
Stephen E. Dowd               |  | Senior Vice President and Chief Financial Officer(Principal Financial and Accounting Officer) |  | January 12, 2012 
|                                                  |  |                                                                                              
|/S/ WILLIAM V. CUDDY
William V. Cuddy             |  | Director                                                                                      |  | December 15, 2009
|                                                  |  |                                                                                              
|/S/ WILLIAM P. HARRINGTON
William P. Harrington   |  | Director                                                                                      |  | December 15, 2009
|                                                  |  |                                                                                              
|/S/ SUSAN A. MASSARO
Susan A. Massaro             |  | Director                                                                                      |  | December 15, 2009
|                                                  |  |                                                                                              
|/S/ CHERI R. MAZZA
Cheri R. Mazza                 |  | Director                                                                                      |  | December 15, 2009
|                                                  |  |                                                                                              
|/S/ MATTHEW G.
MCCROSSON Matthew G. McCrosson     |  | Director                                                                                      |  | December 15, 2009
|                                                  |  |                                                                                              
|/S/ ANNEMARIE V. ROMAGNOLI
Annemarie V. Romagnoli |  | Director                                                                                      |  | December 15, 2009



---

SIGNATURES

Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrant has duly caused this Amendment No. 1 to Form 10-K to be signed on its behalf by the
undersigned, thereunto duly authorized.



CMS BANCORP, INC.By:

/S/    STEPHEN E. DOWDStephen E. Dowd Senior Vice President and Chief Financial Officer (Duly Authorized
Representative)


Date:

January 12, 2012




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EXHIBIT INDEX



|            |  |                                                                                                                                    
|----------- |  | -----------------------------------------------------------------------------------------------------------------------------------
|Exhibit No. |  | Description                                                                                                                        
|            | 
|2.1         |  | Amended and Restated Plan of Conversion and Stock Issuance of Community Mutual Savings Bank. (1)                                   
|            | 
|3.1         |  | Certificate of Incorporation of CMS Bancorp, Inc. (2)                                                                              
|            | 
|3.2         |  | Certificate of Amendment to Certificate of Incorporation filed with the Delaware Secretary of State on February 20, 2009. (3)      
|            | 
|3.3         |  | Bylaws of CMS Bancorp, Inc. (2)                                                                                                    
|            | 
|4.1         |  | Form of Stock Certificate of CMS Bancorp, Inc. (2)                                                                                 
|            | 
|4.2         |  | Form of Option Agreement under the CMS Bancorp, Inc. 2007 Stock Option Plan. (4)                                                   
|            | 
|4.3         |  | Form of Restricted Stock Award Agreement under the CMS Bancorp, Inc. 2007 Recognition and Retention Plan. (4)                      
|            | 
|10.1        |  | Form of Employee Stock Ownership Plan of CMS Bancorp, Inc. (5)                                                                     
|            | 
|10.2        |  | Amended and Restated Employment Agreement between John E. Ritacco and CMS Bancorp, Inc. (6)                                        
|            | 
|10.3        |  | Amended and Restated Employment Agreement between John E. Ritacco and Community Mutual Savings Bank. (6)                           
|            | 
|10.4        |  | Form of Two-Year Change of Control Agreement by and among certain officers, Community Mutual Savings Bank and CMS Bancorp, Inc. (1)
|            | 
|10.5        |  | CMS Bancorp, Inc. 2007 Stock Option Plan. (7)                                                                                      
|            | 
|10.6        |  | CMS Bancorp, Inc. 2007 Recognition and Retention Plan. (7)                                                                         
|            | 
|13.1        |  | CMS Bancorp, Inc. 2009 Annual Report to Shareholders.*                                                                             
|            | 
|14.1        |  | Code of Ethics. (8)                                                                                                                
|            | 
|21.1        |  | Subsidiary of the Registrant*                                                                                                      
|            | 
|23.1        |  | Independent Registered Public Accounting Firms Consent.*                                                                          
|            | 
|31.1        |  | Rule 13a-14(a)/15d-14(a) Certification.**                                                                                          
|            | 
|31.2        |  | Rule 13a-14(a)/15d-14(a) Certification.**                                                                                          
|            | 
|32.1        |  | Section 1350 Certification.*                                                                                                       
|            | 
|32.2        |  | Section 1350 Certification.*                                                                                                       





|* | Filed with the Annual Report on Form 10-K dated December 15, 2009.
|- | ------------------------------------------------------------------

|** | Filed herewith.
|-- | ---------------

|(1) | Incorporated by reference to the amendment to Registration Statement No. 333-139176 on Form SB-2 filed with the Commission on February 2, 2007, as amended.
|--- | -----------------------------------------------------------------------------------------------------------------------------------------------------------

|(2) | Incorporated by reference to the Registration Statement No. 333-139176 on Form SB-2 filed with the Commission on December 7, 2006, as amended.
|--- | ----------------------------------------------------------------------------------------------------------------------------------------------

|(3) | Incorporated by reference to the Registrants Form 8-K filed with the Commission on February 23, 2009.
|--- | ------------------------------------------------------------------------------------------------------

|(4) | Incorporated by reference to the amendment to Registration Statement No. 333-139176 on Form S-8 filed with the Commission on November 30, 2007, as amended.
|--- | -----------------------------------------------------------------------------------------------------------------------------------------------------------

|(5) | Incorporated by reference to the amendment to Registration Statement No. 333-139176 on Form SB-2/A filed with the Commission on January 19, 2007, as amended.
|--- | -------------------------------------------------------------------------------------------------------------------------------------------------------------

|(6) | Incorporated by reference to the Registrants Form 8-K filed with the Commission on July 31, 2008.
|--- | --------------------------------------------------------------------------------------------------

|(7) | Incorporated by reference to the Registrants Proxy Statement filed with the Commission on September 21, 2007.
|--- | --------------------------------------------------------------------------------------------------------------

|(8) | Incorporated by reference to the Registrants Annual Report on Form 10-KSB filed with the Commission on December 28, 2007.
|--- | --------------------------------------------------------------------------------------------------------------------------