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UNITED STATES SECURITIES AND EXCHANGE COMMISSION
 Washington, D.C. 20549
 Form 10-K/A
 (Amendment No. 1)
 þ
    
    ANNUAL REPORT UNDER SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
 For the fiscal year ended December 31, 2009
 o
    
    TRANSITION REPORT UNDER SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
 For the transition period from  to
 Commission file number 333-145939
 CleanTech
Biofuels, Inc.
  Delaware
(State or other jurisdiction of incorporation or organization)
    
    33-0754902
(I.R.S. Employer Identification No.)7386 Pershing Ave., University City, Missouri
(Address of principal executive offices)
    
    63130
(Zip Code)
 (314) 802-8670
 Securities registered under Section 12(b) of the Exchange Act:  Securities registered under Section 12(g) of the Exchange Act:
 o þ
 o þ
 þ o
 o o
 þ
  Large accelerated filer o
    
    Accelerated filer o
    
    Non-accelerated filer o
(Do not check if a smaller reporting company)
    
    Smaller reporting company þ
 o þ
   DOCUMENTS INCORPORATED BY REFERENCE




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CLEANTECH BIOFUELS, INC.
TABLE OF CONTENTS
 PAGEPART III
    
    
    3ITEM 10. Directors, Executive Officers and Corporate Governance
    
    
    3ITEM 11. Executive Compensation
    
    
    5ITEM 12. Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters
    
    
    9ITEM 13. Certain Relationships and Related Transactions and Director Independence
    
    
    10ITEM 14. Principal Accountant Fees and Services
    
    
    11PART IV
    
    
    11ITEM 15. Exhibits and Financial Statement Schedules
    
    
    11Signatures
    
    
    12Index to Exhibits
    
    
    13Exhibit 31.1Exhibit 31.2Exhibit 32.1Exhibit 32.2
   2




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Explanatory Note:
   
 PART III.
 
 ITEM 10.
    
    DIRECTORS, EXECUTIVE OFFICERS AND CORPORATE GOVERNANCE
   Class III: Terms expiring in 2010
 Service asName
    
    Age
    
    Principal Occupation
    
    Director SinceEdward P. Hennessey
    
    
    51
    
    
    Mr. Hennessey currently
is Chief Executive
Officer and President of
the Company, and serves
as Chairman of the Board
of Directors. Mr.
Hennessey has been the
President and CEO of SRS
Energy since 2003 and as
President of
Supercritical Recovery
Systems, Inc. prior to
that time since 2002.
Mr. Hennessey began his
career in Finance with
Shearson Lehman Brothers
in 1986 and worked in
the securities industry
from 1986 until 2000.
    
    
    2007
  3




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Class I: Terms expiring in 2011
 Service asName
    
    Age
    
    Principal Occupation
    
    Director SincePaul Simon, Jr.
    
    
    51
    
    
    Mr. Simon is a licensed
attorney practicing in St.
Louis, Missouri and has been
a partner in the firm,
Sauerwein, Simon, &
Blanchard, P.C. since 2006.
Prior to that time, he was a
partner with the firm
Helfrey, Simon and Jones,
P.C. from 1991 until 2006.
Mr. Simon is a graduate of
the University of Missouri
where he received his B.S. in
Business Administration and
St. Louis University School
of Law where he received his
J.D.
    
    
    2007Jose Bared, Sr.
    
    
    68
    
    
    Mr. Bared began his career as
an engineer and in 1968
founded The Bared Company, a
Mechanical and Electrical
Engineering and Design
company. Mr. Bared was also a
member of the founding group
that purchased Republic
National Bank of Miami in
1971. Mr. Bared served as a
director of the bank from
1971 until its sale in 1998.
Currently Mr. Bared serves
on the Board of Directors of
Jackson  United Petroleum,
a natural gas producer
operating in Kentucky and
Pennsylvania. He has served
on the Board of Trustees for
the University of Miami for
the past 30 years. He also
has served on the Board of
Governors of the Sylvester
Cancer Center for the past 15
years and is a life member of
the center. Mr. Bared holds a
B.S. in Mechanical
Engineering from the
University of Miami.
    
    
    2010
 Class II: Terms expiring in 2012
 Service asName
    
    Age
    
    Principal Occupation
    
    Director SinceJackson Nickerson,
Phd.
    
    
    47
    
    
    Dr. Nickerson is the
Frahm Family
Professor of
Organization and
Strategy at
Washington
Universitys Olin
Business School in
St. Louis and has
been at the
university since
1996. He consults
with numerous profit
and not-for-profit
organizations on
strategy development.
Dr. Nickerson
launched and is
currently a director
of nformd.net, a
privately held new
media company. He has
a B.S. in mechanical
engineering from
Worcester Polytechnic
Institute and an M.S.
in mechanical
engineering, an
M.B.A. and a Ph.D.
from the University
of California,
Berkeley.
    
    
    2009David Bransby, Phd
    
    
    58
    
    
    Dr. Bransby is a
Professor of Energy
Crops and Bioenergy
in the Department of
Agronomy and Soils at
Auburn University
where he has taught
and conducted
research since 1987.
He has more than 30
years of experience
in agronomic
research, and has
spent 22 years
specializing in the
production and
processing of energy
crops. He serves on
the editorial boards
of two international
bioenergy journals,
and consults for
several private
bioenergy companies.
    
    
    2009
 Audit Committee
  Compensation Committee
   4




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Nomination of Directors
   Code of Ethics
  
 ITEM 11.
    
    EXECUTIVE COMPENSATION
 Compensation Discussion and Analysis
  Our Executive Compensation Policy
  
    
    provide fair and reasonable compensation that meets the competitive environment for executive talent;
    
    help motivate the members of our executive team for excellent performance; and
    
    align the interests of our executive team members with those of our stockholders and the long-term
success of our company.
  5




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Elements of our Executive Compensation Program
  Base Salary 
 Bonuses 
 Long-Term Incentive Compensation 
  Executive Perquisites 
  6




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Tax and Accounting Implications
  Summary Compensation Table
  (1) StockName and Principal Position(s)
    
    Year
    
    
    Salary ($)
    
    
    Options ($)
    
    
    Total ($)Edward P. Hennessey, President and CEO
    
    
    2007
    
    
    $
    63,000
    
    
    $
    38,843
    
    
    $
    101,8432008
    
    
    
    68,000
    
    
    
    103,574
    
    
    
    171,5742009
    
    
    
    109,000
    
    
    
    227,182
    
    
    
    336,182Michael D. Kime, General Counsel and COO
    
    
    2007
    
    
    
    
    
    
    
    13,811
    
    
    
    13,8112008
    
    
    
    24,000
    
    
    
    39,678
    
    
    
    63,6782009
    
    
    
    109,000
    
    
    
    76,884
    
    
    
    185,884Thomas Jennewein, Chief Financial Officer
    
    
    2007
    
    
    
    
    
    
    
    13,811
    
    
    
    13,8112008
    
    
    
    10,000
    
    
    
    36,623
    
    
    
    46,6232009
    
    
    
    92,000
    
    
    
    45,880
    
    
    
    137,880
 (1)
    
    The assumptions made when calculating the amounts in this column are found in footnote
10 to the Consolidated Financial Statements of Cleantech Biofuels, Inc., as filed with the
SEC on Form 10-K for 2009. The amounts represent the SFAS 123(R) accounting cost that the
Company recorded in its Statements of Operations in each year.  7




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Outstanding Equity Awards at Fiscal Year-End
  Option Awards
    
    
    Stock AwardsNumber of
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    MarketNumber of
    
    
    Securities
    
    
    
    
    
    
    
    
    
    
    Number
    
    
    value ofSecurities
    
    
    Underlying
    
    
    
    
    
    
    
    
    
    
    of Shares
    
    
    shares orUnderlying
    
    
    Unexercised
    
    
    
    
    
    
    
    
    
    
    or Units
    
    
    units ofUnexercised
    
    
    Options (#)-
    
    
    Option
    
    
    Option
    
    
    of Stock
    
    
    stock thatOptions (#)-
    
    
    Unexercisable
    
    
    Exercise
    
    
    Expiration
    
    
    that have
    
    
    haveGrant Date
    
    
    Exercisable
    
    
    (3)
    
    

Price
($)
    
    
    Date
    
    
    vested (#)
    
    
    vestedEdward P. Hennessey
    
    
    8/31/2007
    
    
    
    1,500,000
    (1)
    
    
    750,000
    
    
    $
    0.15
    
    
    
    8/31/2014
    
    
    
    
    
    
    $
    12/4/2008
    
    
    
    400,000
    (2)
    
    
    800,000
    
    
    $
    0.15
    
    
    
    12/4/2015
    
    
    
    
    
    
    $
    12/4/2008
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    60,000
    (4)
    
    $
    Michael D. Kime
    
    
    8/31/2007
    
    
    
    533,334
    (1)
    
    
    266,666
    
    
    $
    0.15
    
    
    
    8/31/2014
    
    
    
    
    
    
    $
    12/4/2008
    
    
    
    266,667
    (2)
    
    
    533,333
    
    
    $
    0.36
    
    
    
    12/4/2015
    
    
    
    
    
    
    $
    12/4/2008
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    60,000
    (4)
    
    $
    Thomas G. Jennewein
    
    
    8/31/2007
    
    
    
    533,334
    (1)
    
    
    266,666
    
    
    $
    0.15
    
    
    
    8/31/2014
    
    
    
    
    
    
    $
    12/4/2008
    
    
    
    133,333
    (2)
    
    
    266,667
    
    
    $
    0.36
    
    
    
    12/4/2015
    
    
    
    
    
    
    $
    12/4/2008
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    60,000
    (4)
    
    $
    
 (1)
    
    This option grant vests in three equal annual installments beginning on August 31, 2008.(2)
    
    This option grant vests in three equal annual installments beginning on August 31, 2009.(3)
    
    The options shown in this column are nonvested as of December 31, 2009.(4)
    
    This stock award was granted on December 4, 2008. Each officer issued promissory notes with an exercise price of $0.36. Option Exercises and Stock Vested
 Option Awards
    
    
    Stock AwardsNumber of
    
    
    
    
    
    
    Number of
    
    
    
    
    
    
    Number ofShares
    
    
    Value
    
    
    Shares
    
    
    Value Upon
    
    
    Shares
    
    
    ValueAcquired on
    
    
    Realized on
    
    
    Acquired on
    
    
    Vesting ($)
    
    
    Acquired on
    
    
    Realized onExercise (#)
    
    
    Exercise ($)
    
    
    Vesting (#)
    
    
    (1)
    
    
    Vesting (#)
    
    
    Vesting ($)Edward P. Hennessey
    
    
    
    
    
    $
    
    
    
    
    750,000
    
    
    $
    562,500
    
    
    
    60,000
    
    
    $
    
    
    
    $
    
    
    
    
    750,000
    
    
    $
    
    (2)
    
    
    $
    
    
    
    
    400,000
    
    
    $
    
    (2)Michael D. Kime
    
    
    
    
    
    $
    
    
    
    
    266,667
    
    
    $
    200,000
    
    
    
    60,000
    
    
    $
    
    
    
    $
    
    
    
    
    266,667
    
    
    $
    
    (2)
    
    
    $
    
    
    
    
    266,667
    
    
    $
    
    (2)Thomas G. Jennewein
    
    
    
    
    
    $
    
    
    
    
    266,667
    
    
    $
    200,000
    
    
    
    60,000
    
    
    $
    
    
    
    $
    
    
    
    
    266,667
    
    
    $
    
    (2)
    
    
    $
    
    
    
    
    133,333
    
    
    $
    
    (2)
 (1)
    
    The values reflect the market value of Cleantech Biofuels, Inc. common stock as of the vesting dates. These prices ranged from $0.11 to $0.90.(2)
    
    The price of our common stock on these vesting dates was less than the exercise price of the options. Pension Benefits 
 Nonqualified Deferred Compensation 
 Director Compensation 
  8




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Potential Payments Upon Termination or Change-in-Control
     
 ITEM 12.
    
    SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT AND RELATED STOCKHOLDER MATTERS
  Name and Address of
    
    Amount and Nature ofBeneficial Owner
    
    Beneficial Ownership
    
    
    Percent of ClassEdward P. Hennessey, Jr. (1)
    
    
    7,443,275
    
    
    
    11.2
    %7310 Forsyth Ave.Clayton, MO 63105SRS Legacy Trust(2)
    
    
    7,972,214
    
    
    
    12.0
    %RAM Resources, L.L.C.(3)
    
    
    4,303,589
    
    
    
    6.5
    %13397 Lakefront DriveEarth City, Missouri 63045
 (1)
    
    Amount represents shares owned by Supercritical Recovery Systems, Inc., of which Mr. Hennessey serves as President and a Member of the Board of Directors.(2)
    
    SRS Legacy Trust is an irrevocable trust of which Edward P. Hennessey, Jr. is a beneficiary. Michael Hennessey, Mr. Hennesseys brother, has sole voting power, and Paul Simon, Jr., one of our directors, has sole dispositive power with respect to these shares.(3)
    
    Rodney H. Thomas, as Trustee of the Trust which is the majority owner of RAM Resources, L.L.C., has controlling voting and dispositive power over these shares.  9




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SECURITY OWNERSHIP OF MANAGEMENT
  Amount and Nature of
    
    
    Percent ofName and Address of Beneficial Owner
    
    Beneficial Ownership
    
    
    ClassEdward P. Hennessey, Jr.
    
    
    9,403,275
    (1)
    
    
    13.8
    %Michael D. Kime
    
    
    860,001
    (2)
    
    
    1.3
    %Thomas Jennewein
    
    
    726,667
    (2)
    
    
    1.1
    %Jackson Nickerson
    
    
    126,148
    (3)
    
    
    *
    %David Bransby
    
    
    74,997
    (2)
    
    
    *
    %Jose Bared
    
    
    33,332
    (2)
    
    
    *
    %Paul Simon
    
    
    267,935
    (4)
    
    
    *
    %Total owned by All Executive Officers and Directors
    
    
    11,492,355
    
    
    
    16.4
    %
 *
    
    Less than 1%.(1)
    
    Includes the shares described in footnote 1 to the Security Ownership of Certain
Beneficial Owners table and the vested portion and the portion that will vest within 60
days hereof of shares of options and restricted stock.(2)
    
    Amounts represent the vested portion and the portion that will vest within 60 days
hereof of shares of options and restricted stock.(3)
    
    Amount includes 74,997 shares vested and the portion that will vest within 60 days
hereof of shares of options and restricted stock and shares held individually.(4)
    
    Amount includes 190,000 shares vested and the portion that will vest within 60 days
hereof of shares of options and restricted stock and shares held individually.  
 ITEM 13.
    
    CERTAIN RELATIONSHIPS AND RELATED-PARTY TRANSACTIONS AND DIRECTOR INDEPENDENCE
       10




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Determination of Director Independence
  
 ITEM 14.
    
    PRINCIPAL ACCOUNTANT FEES AND SERVICES
  For the years ended December 31,2009
    
    
    2008Audit Fees (1)
    
    $
    8,800
    
    
    $
    9,805Tax Fees
    
    
    
    
    
    
    Audit-Related Fees
    
    
    
    
    
    
    All Other Fees
    
    
    
    
    
    
    Total Fees
    
    $
    8,800
    
    
    $
    9,805
 (1)
    
    Includes annual financial statement audit. 
 PART IV.
 
 ITEM 15.
    
    EXHIBITS AND FINANCIAL STATEMENT SCHEDULES
  ExhibitNumber
    
    Description31.1
    
    
    Certification of Chief Executive Officer pursuant to Rule 13a-14(a)
and Rule 15d-14(a) of the Securities
Exchange Act, as amended31.2
    
    
    Certification of principal financial officer pursuant to Rule
13a-14(a) and Rule 15d-14(a) of the Securities
Exchange Act, as amended32.1
    
    
    Certificate (Pursuant to 18 U.S.C. Section 1350 as Adopted Pursuant
to Section 906 of the Sarbanes-Oxley Act of 2002) of Chief Executive
Officer32.2
    
    
    Certificate (Pursuant to 18 U.S.C. Section 1350 as Adopted Pursuant
to Section 906 of the Sarbanes-Oxley Act of 2002) of principal
financial officer
  11




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SIGNATURES
  CleanTech Biofuels,
Inc.

(registrant)April 30, 2010
    By:
    /s/ Edward P. Hennessey, Jr.Edward P. Hennessey, Jr.Chief Executive OfficerApril 30, 2010
    By:
    /s/ Thomas G. JenneweinThomas G. JenneweinChief Financial Officer  12




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ExhibitNumber
    
    Description31.1
    
    
    Certification of Chief Executive Officer pursuant to Rule 13a-14(a)
and Rule 15d-14(a) of the Securities
Exchange Act, as amended31.2
    
    
    Certification of principal financial officer pursuant to Rule
13a-14(a) and Rule 15d-14(a) of the Securities
Exchange Act, as amended32.1
    
    
    Certificate (Pursuant to 18 U.S.C. Section 1350 as Adopted Pursuant
to Section 906 of the Sarbanes-Oxley Act of 2002) of Chief Executive
Officer32.2
    
    
    Certificate (Pursuant to 18 U.S.C. Section 1350 as Adopted Pursuant
to Section 906 of the Sarbanes-Oxley Act of 2002) of principal
financial officer
  13