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UNITED STATES
SECURITIES AND EXCHANGE COMMISSION
 Washington, D.C. 20549
 FORM 10-K/A
 (Amendment No. 2)
 Annual Report Pursuant to Section 13 or 15(d)
of the Securities Exchange Act of 1934
 For the fiscal year ended September 30, 2008
    
    Commission File Number 0-20600
 ZOLTEK COMPANIES, INC.
  Missouri
    
    43-1311101(State or other jurisdiction of
    
    (I.R.S. Employer Identification No.)incorporation or organization)3101 McKelvey Road, St. Louis, Missouri
    
    63044(Address of principal executive offices)
    
    (Zip Code)
     o þ
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  Large Accelerated Filer þ
    
    Accelerated Filer o
    
    Non-Accelerated Filer o
    
    Smaller reporting company o
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   DOCUMENTS INCORPORATED BY REFERENCE
  Document
    
    Part of Form 10-KProxy Statement for the 2009
Annual Meeting of Shareholders
    
    III




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TABLE OF CONTENTS  PART IVItem 15. Exhibits and Financial Statement ScheduleSIGNATURESExhibit IndexExhibit 10.11Exhibit 31.1Exhibit 31.2Exhibit 32.1Exhibit 32.2    Table of Contents  EXPLANATORY NOTE
    2




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PART IV
 
 Item 15. Exhibits and Financial Statement Schedule
                Column A
    
    Column B
    
    
    Column C
    
    
    Column D
    
    
    Column EAdditionsBalance at
    
    
    Charged to
    
    
    Charged to
    
    
    
    
    
    
    Balance atbeginning
    
    
    costs and
    
    
    other accounts
    
    
    Deductions
    
    
    endof period
    
    
    expenses
    
    
    describe
    
    
    describe
    
    
    of periodReserve for doubtful accounts
    
    $
    781
    
    
    $
    1,300
    
    
    $
    
    
    
    $
    327
    
    
    $
    1,754Reserve for inventory valuation
    
    $
    645
    
    
    $
    
    
    
    $
    
    
    
    $
    145
    (7)
    
    $
    500Deferred tax valuation
    
    $
    29,758
    
    
    $
    1,057
    
    
    $
    
    
    
    $
    
    
    
    $
    30,815
 
    Column A
    
    Column B
    
    
    Column C
    
    
    Column D
    
    
    Column EAdditionsBalance at
    
    
    Charged to
    
    
    Charged to
    
    
    
    
    
    
    Balance atbeginning
    
    
    costs and
    
    
    other accounts
    
    
    Deductions
    
    
    endof period
    
    
    expenses
    
    
    describe
    
    
    describe
    
    
    of periodReserve for doubtful accounts
    
    $
    729
    
    
    $
    52
    
    
    $
    
    
    
    $
    
    
    
    $
    781Reserve for inventory valuation
    
    $
    1,300
    
    
    $
    
    
    
    $
    
    
    
    $
    655
    (7)
    
    $
    645Deferred tax valuation
    
    $
    34,217
    
    
    $
    
    
    
    $
    628
    (5)
    
    $
    5,087(
    3)(4)(6)
    
    $
    29,758
 
  3




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##### Table of Contents



Column A
    
    Column B
    
    
    Column C
    
    
    Column D
    
    
    Column EAdditionsBalance at
    
    
    Charged to
    
    
    Charged to
    
    
    
    
    
    
    Balance atbeginning
    
    
    costs and
    
    
    other accounts
    
    
    Deductions
    
    
    endof period
    
    
    expenses
    
    
    describe
    
    
    describe
    
    
    of periodReserve for doubtful accounts
    
    $
    718
    
    
    $
    306
    
    
    $
    
    
    
    $
    295
    (1)
    
    $
    729Reserve for inventory valuation
    
    $
    3,100
    
    
    $
    
    
    
    $
    
    
    
    $
    1,800
    (2)
    
    $
    1,300Deferred tax valuation
    
    $
    22,401
    
    
    $
    14,233
    
    
    $
    
    
    
    $
    2,417
    (3)
    
    $
    34,217
 
 (1)
    
    Write-off of uncollectible receivable, net of recovery.(2)
    
    Reduction in inventory reserve for inventory items related to discontinued operations.(3)
    
    Expiration of capital loss carryforward and utilization against current foreign income taxes
payable.(4)
    
    Removal of NOLs related to non-qualified stock options and the related valuation allowance.(5)
    
    Addition of a valuation allowance on the Texas tax credits that were created from prior years
Texas NOL. The credits are created
and calculated under the newly enacted Texas margin tax law.(6)
    
    Prior year true-ups.(7)
    
    Company used and sold materials for which reserves were established primarily for slow moving
product.    4




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SIGNATURES
  ZOLTEK COMPANIES, INC.
(Registrant)By

/s/ Zsolt RumyZsolt Rumy, Chairman of the Board, President andChief Executive OfficerBy

/s/ Andrew W. WhippleAndrew W. Whipple, Chief Financial Officer   5




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Exhibit Index
 ExhibitNumber
    
    Description3.1
    
    
    Restated Articles of Incorporation of
the Registrant dated October 7, 1992,
filed as Exhibit 3.1 to Registrants
Registration Statement on Form S-3
(Reg. No.333-143996) and incorporated
herein by reference.3.2
    
    
    Certificate of Amendment of Restated
Articles of Incorporation of the
Registrant dated February 15, 1996,
filed as Exhibit 3.2 to Registrants
Registration Statement on Form S-3
(Reg. No.333-143996) and incorporated
herein by reference.3.3
    
    
    Certificate of Amendment of Restated
Articles of Incorporation of the
Registrant dated February 7, 1997,
filed as Exhibit 3.3 to Registrants
Registration Statement on Form S-3
(Reg. No.333-143996) and incorporated
herein by reference.3.4
    
    
    Restated By-Laws of the Registrant
dated September 22, 1992, filed as
Exhibit 3.4 to Registrants
Registration Statement on Form S-3
(Reg. No.333-143996) and incorporated
herein by reference.4.1
    
    
    Form of certificate for Common Stock,
filed as Exhibit 4.1 to Registrants
Registration Statement on Form S-1
(Reg. No. 33-51142) and incorporated
herein by reference.4.2
    
    
    Form of Warrant, dated May 11, 2001,
issued to Southwest Bank of St. Louis
with respect to 12,500 shares of
Registrants Common Stock, filed as
Exhibit 4.2 to Registrants Annual
Report on Form 10-K for the year ended
September 30, 2001 and incorporated
herein by reference.4.3
    
    
    Securities Purchase Agreement, dated as
of December 19, 2003, by and among
Zoltek Companies, Inc. and the
investors named therein, filed as
Exhibit 4.6 to Registrants Annual
Report on Form 10-K for the fiscal year
ended September 30, 2003 and
incorporated herein by reference.4.4
    
    
    Form of 6% Convertible Debenture, filed
as Exhibit 4.7 to Registrants Annual
Report on Form 10-K for the fiscal year
ended September 30, 2003 and
incorporated herein by reference.4.17
    
    
    Form of Warrant, filed as Exhibit 4.8
to Registrants Annual Report on
Form 10-K for the fiscal year ended
September 30, 2003 and incorporated
herein by reference.4.18
    
    
    Securities Purchase Agreement, dated as
of March 11, 2004, by and among Zoltek
Companies, Inc. and the investors named
therein, filed as Exhibit 4.2 to
Registrants Registration Statement on
Form S-3 (Reg. No. 333-115043) and
incorporated herein by reference.4.19
    
    
    Form of 6% Convertible Debenture, filed
as Exhibit 4.3 to Registrants
Registration Statement on Form S-3
(Reg. No. 333-115043) and incorporated
herein by reference.4.20
    
    
    Form of Warrant, filed as Exhibit 4.4
to Registrants Registration Statement
on Form S-3 (Reg. No. 333-115043) and
incorporated herein by reference.4.21
    
    
    Loan and Warrant Agreement, dated as of
October 14, 2004, filed as Exhibit 4.1
to Registrants Current Report on
Form 8-K dated October 19, 2004 and
incorporated herein by reference.4.22
    
    
    Security Agreement, dated as of
October 14, 2004, filed as Exhibit 4.3
to Registrants Current Report on
Form 8-K dated October 19, 2004 and
incorporated herein by reference.4.23
    
    
    Mortgage Agreement, dated as of
October 14, 2004, filed as Exhibit 4.4
to Registrants Current Report on
Form 8-K dated October 19, 2004 and
incorporated herein by reference.4.24
    
    
    Form of Warrant, filed as Exhibit 4.5
to Registrants Current Report on
Form 8-K dated October 19, 2004 and
incorporated herein by reference.4.25
    
    
    Loan and Warrant Agreement, dated as of
February 9, 2005, by and among the
Registrant, the Lenders and the Agent,
filed as Exhibit 4.1 to the
Registrants Quarterly Report on
Form 10-Q for the quarter ended
December 31, 2004 and incorporated
herein by reference.4.26
    
    
    Form of Senior Convertible Note, dated
as of February 9, 2005, filed as
Exhibit 4.2 to the Registrants
Quarterly Report on Form 10-Q for the
quarter ended December 31, 2004 and
incorporated herein by reference.4.27
    
    
    Form of Warrant, dated as of
February 9, 2005, filed as Exhibit 4.3
to the Registrants Quarterly Report on
Form 10-Q for the quarter ended
December 31, 2004 and incorporated
herein by reference.4.28
    
    
    Form of Registration Rights Agreement,
dated as of February 9, 2005, filed as
Exhibit 4.4 to the Registrants
Quarterly Report on Form 10-Q for the
quarter ended December 31, 2004 and
incorporated herein by reference.4.29
    
    
    Loan and Warrant Agreement, dated as of
September 29, 2005, among the
Registrant, the Lenders and the Agent,
filed as Exhibit 4.1 to the
Registrants Current Report on Form 8-K
dated September 29, 2005 and
incorporated herein by reference.4.30
    
    
    Form of Note, filed as Exhibit 4.2 to
the Registrants Current Report on
Form 8-K dated September 29, 2005 and
incorporated herein by reference.4.31
    
    
    Form of Warrant, filed as
Exhibit 4.3 to the Registrants
Current Report on Form 8-K dated
September 29, 2005 and incorporated
herein by reference.4.32
    
    
    Registration Rights Agreement, dated as of
September 30, 2005, by and among the Registrant and
the Lenders parties thereto, filed as Exhibit 4.4 to
the Registrants Current Report on Form 8-K dated
September 29, 2005 and incorporated herein by
reference.
  6




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ExhibitNumber
    
    Description4.33
    
    
    Waiver and Consent, dated as of February 3, 2006, by and
among the Registrant and the Lender parties thereto, filed as
Exhibit 4.5 to the Registrants Current Report on Form 8-K
dated February 6, 2006, and incorporated herein by reference.4.34
    
    
    Amendment No. 1 to Loan and Warrant Agreement and
Registration Rights Agreement among the Registrant and the
Lender parties thereto, filed as Exhibit 4.2 to the
Registrants Current Report on Form 8-K dated April 28, 2006
and incorporated herein by reference.4.35
    
    
    Form of Note, filed as Exhibit 4.3 to the Registrants
Current Report on Form 8-K dated April 28, 2006 and
incorporated herein by reference.4.36
    
    
    Form of Warrant, filed as Exhibit 4.4 to the Registrants
Current Report on Form 8-K dated April 28, 2006 and
incorporated herein by reference.4.37
    
    
    Amendment No. 2 to Loan and Warrant Agreement and
Registration Rights Agreement, dated as of December 14, 2006,
among the Registrant and the Lenders, filed as Exhibit 4.3 to
the Registrants Current Report on Form 8-K dated
December 14, 2006 and incorporated herein by reference.4.38
    
    
    Form of Warrant, filed as Exhibit 4.4 to the Registrants
Current Report on Form 8-K dated December 14, 2006 and
incorporated herein by reference.10.1
    
    
    Zoltek Companies, Inc.
Long Term Incentive Plan filed as Appendix B to Registrants definitive Proxy Statement
for the 1997 Annual Meeting of Shareholders is incorporated herein by this reference.*10.2
    
    
    Zoltek Companies, Inc.
Amended and Restated Directors Stock Option Plan filed as Exhibit 10.1 to Registrants
Quarterly Report on Form 10-Q dated August 13, 1999 is incorporated herein by this reference.*10.3
    
    
    Credit Agreement, dated as of May 11, 2001, between Southwest
Bank of St. Louis and Zoltek Companies, Inc., Zoltek
Corporation, Cape Composites, Inc., Engineering Technology
Corporation, Zoltek Properties, Inc., and Hardcore Composites
Operations, LLC, filed as Exhibit 10.1 to Registrants
Quarterly Report on Form 10-Q for the quarter ended June 30,
2001, is incorporated herein by reference.10.4
    
    
    First Amendment to Credit Agreement, dated as of February 13,
2003, by and among Zoltek Companies, Inc., Zoltek
Corporation, Cape Composites, Inc., Engineering Technology
Corporation, Zoltek Properties, Inc. and Southwest Bank of
St. Louis, filed as Exhibit 10.1 to Registrants Current
Report on Form 8-k dated February 18, 2003 is incorporated
herein by reference.10.5
    
    
    Zoltek Companies, Inc. 2003 Long-Term Equity Incentive Plan,
filed as Appendix A to Registrants definitive proxy
statement for the 2002 Annual Meeting of Shareholders is incorporated herein by this reference*10.6
    
    
    Second Amendment to Credit Agreement, dated as of January 13,
2003, by and among Zoltek Companies, Inc., Zoltek
Corporation, Cape Composites, Inc., Engineering Technology
Corporation, Zoltek Properties, Inc. and
Southwest Bank of St. Louis filed as Exhibit 10.14 to
Registrants Annual Report on Form 10-K for the fiscal year
ended September 30, 2003, is incorporated herein by this
reference10.7
    
    
    Zoltek Companies, Inc. 2008 Director Incentive Plan, filed as
Appendix A to the Registrants Proxy Statement on Schedule
14A filed on January 2, 2008 and incorporated herein by this
reference.*10.8
    
    
    Zoltek Companies, Inc. 2008 Long Term Incentive Plan, filed
as Appendix B to the Registrants Proxy Statement on Schedule
14A filed on January 2, 2008 and incorporated herein by this
reference.*10.9
    
    
    Employment Agreement, dated March 1, 2008, between the
Registrant and Karen Bomba, filed as Exhibit 10.1 to the
Registrants Quarterly Report on Form 10-Q for the quarter
ended March 31, 2008 and incorporated herein by reference.10.10
    
    
    Employment Agreement, dated November 26, 2008, between the
Registrant and Andrew W. Whipple.**10.11
    
    
    Second Trade Agreement dated as of May 29, 2007, between
Vestas Wind Systems A/S and Zoltek Companies, Inc. filed
herewith.***21
    
    
    Subsidiaries of the Registrant filed as Exhibit 21 to the
Registrants Annual Report on Form 10-k for the fiscal year
ended September 30, 2007 and incorporated herein by
reference.23.1
    
    
    Consent of Grant Thornton LLP.**23.2
    
    
    Consent of PricewaterhouseCoopers LLP.**31.1
    
    
    Certification of Chief Executive Officer pursuant to Rule
13a-14(a) under the Securities Exchange Act of 1934, as
amended is filed herewith.31.2
    
    
    Certification of Chief Financial Officer pursuant to Rule
13a-14(a) under the Securities Exchange Act of 1934, as
amended is filed herewith.32.1
    
    
    Certification of Chief Executive Officer pursuant to 18
U.S.C. Section 1350, as adopted pursuant to Section 906 of
the Sarbanes-Oxley Act of 2002 is filed herewith.32.2
    
    
    Certification of Chief Financial Officer pursuant to 18
U.S.C. Section 1350, as adopted pursuant to Section 906 of
the Sarbanes-Oxley Act of 2002 is filed herewith.
 
 *
    
    Management compensatory plan or arrangement**
    
    Previously filed***
    
    Confidential portions of this exhibit have been redacted and filed separately with
the Securities and Exchange
Commission pursuant to a confidential treatment request in accordance with Rule
24b-2 of the Securities Exchange
Act of 1934, as amended.  7