UNITED
STATES




SECURITIES
AND EXCHANGE COMMISSION


WASHINGTON,
D.C. 20549








FORM
10-Q





(MARK
ONE)





x QUARTERLY REPORT
PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES AND EXCHANGE ACT OF
1934





FOR THE
QUARTERLY PERIOD ENDED March 31, 2009





OR





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





COMMISSION
FILE NUMBER: 0-12627





GLOBAL
CLEAN ENERGY HOLDINGS, INC.


(Exact
name of registrant as specified in its charter)







Utah
              
              
              
              87-0407858(State
      or other jurisdiction of
                incorporation
      or organization)
              
              
              
              (I.R.S.
      Employer
                Identification
      Number)6033
      W. Century Blvd, Suite 895,
                Los
      Angeles, California 90045(Address
      of principal executive offices)(310)
      641-4234Issuer’s
      telephone number:







(Former
Name or Former Address, if Changed Since Last Report)





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 xNo  ̈ .





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  ̈ No  ̈





Indicate
by check mark whether the registrant is a large accelerated filer, an
accelerated filer, a non-accelerated filer, or a smaller reporting
company.





Large
      accelerated filer  ̈
            Accelerated
      filer  ̈Non-accelerated
      filer  ̈
            Smaller
      reporting company x





Indicate
the number of shares outstanding of each of the registrant's classes of common
stock, as of the latest practicable date: As of May 15, 2009, the issuer had
229,381,338 shares of common stock outstanding, which includes 3,915,016 shares
of common stock currently held in escrow.





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












GLOBAL
CLEAN ENERGY HOLDINGS, INC.


For
the quarter ended March 31, 2009


FORM
10-Q





TABLE
OF CONTENTS





PART
      IITEM
      1.
                FINANCIAL
      STATEMENTS
                1ITEM
      2.
                MANAGEMENT’S
      DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF
      OPERATIONS
                16ITEM
      3.
                QUANTITATIVE
      AND QUALITATIVE DISCLOSURE ABOUT MARKET RISK
                22ITEM
      4T.
                CONTROLS
      AND PROCEDURES
                22PART
      IIITEM
      1.
                LEGAL
      PROCEEDINGS
                22ITEM
      1A
                RISK
      FACTORS
                22ITEM
      2.
                UNREGISTERED
      SALES OF EQUITY SECURITIES AND USE OF PROCEEDS
                23ITEM
      3.
                DEFAULTS
      UPON SENIOR SECURITIES
                23ITEM
      4.
                SUBMISSION
      OF MATTERS TO A VOTE OF SECURITY HOLDERS
                23ITEM
      5.
                OTHER
      INFORMATION
                23ITEM
      6.
                EXHIBITS
                23








PART
I




ITEM 1.
  FINANCIAL STATEMENTS.


GLOBAL
CLEAN ENERGY HOLDINGS, INC. AND SUBSIDIARIES
 (A
Development Stage Company)
 CONDENSED
CONSOLIDATED BALANCE SHEETS
 (Unaudited)
  March 31,
                              
                              
                              December 31,2009
                              
                              
                              2008ASSETSCURRENT
      ASSETSCash
      and cash equivalents
                              
                              $
                              874,668
                              
                              
                              $
                              291,309Accounts
      receivable
                              
                              
                              20,000
                              
                              
                              
                              -Other
      current assets
                              
                              
                              126,498
                              
                              
                              
                              131,715Total
      Current Assets
                              
                              
                              1,021,166
                              
                              
                              
                              423,024PROPERTY
      AND EQUIPMENTLand
                              
                              
                              2,051,282
                              
                              
                              
                              2,051,282Plantation
      development costs
                              
                              
                              2,665,604
                              
                              
                              
                              2,117,061Plantation
      equipment
                              
                              
                              509,037
                              
                              
                              
                              509,037Office
      equipment
                              
                              
                              10,993
                              
                              
                              
                              10,9935,236,916
                              
                              
                              
                              4,688,373Less
      accumulated depreciation
                              
                              
                              (33,384
                              )
                              
                              
                              (22,296
                              )5,203,532
                              
                              
                              
                              4,666,077OTHER
      ASSETS
                              
                              
                              2,691
                              
                              
                              
                              2,691TOTAL
      ASSETS
                              
                              $
                              6,227,389
                              
                              
                              $
                              5,091,792LIABILITIES
      AND EQUITY (DEFICIT)CURRENT
      LIABILITIESAccounts
      payable
                              
                              $
                              2,067,021
                              
                              
                              $
                              1,890,999Accrued
      payroll and payroll taxes
                              
                              
                              1,277,502
                              
                              
                              
                              1,158,808Accrued
      interest payable
                              
                              
                              603,134
                              
                              
                              
                              522,097Accrued
      return on noncontrolling interest
                              
                              
                              231,537
                              
                              
                              
                              138,014Secured
      promissory note
                              
                              
                              475,000
                              
                              
                              
                              460,000Notes
      payable to shareholders
                              
                              
                              56,000
                              
                              
                              
                              56,000Convertible
      notes payable
                              
                              
                              193,200
                              
                              
                              
                              193,200Research
      and development obligation
                              
                              
                              2,443,480
                              
                              
                              
                              2,607,945Total
      Current Liabilities
                              
                              
                              7,346,874
                              
                              
                              
                              7,027,063MORTGAGE
      NOTE PAYABLE
                              
                              
                              2,051,282
                              
                              
                              
                              2,051,282EQUITY
      (DEFICIT)Global
      Clean Energy Holdings, Inc. equity (deficit)Preferred
      stock - no par value; 50,000,000 shares authorizedSeries
      B, convertible; 13,000 shares issued or subscribed(aggregate
      liquidation preference of $1,300,000)
                              
                              
                              1,290,735
                              
                              
                              
                              1,290,735Common
      stock, no par value; 500,000,000 shares authorized;224,813,819
      shares issued and outstanding
                              
                              
                              17,634,474
                              
                              
                              
                              17,634,474Additional
      paid-in capital
                              
                              
                              3,732,608
                              
                              
                              
                              3,672,724Deficit
      accumulated prior to the development stage
                              
                              
                              (1,399,577
                              )
                              
                              
                              (1,399,577
                              )Deficit
      accumulated during the development stage
                              
                              
                              (27,211,019
                              )
                              
                              
                              (27,146,931
                              )Total
      Global Clean Energy Holdings, Inc. Stockholders' Deficit
                              
                              
                              (5,952,779
                              )
                              
                              
                              (5,948,575
                              )Noncontrolling
      interest
                              
                              
                              2,782,012
                              
                              
                              
                              1,962,022Total
      equity (deficit)
                              
                              
                              (3,170,767
                              )
                              
                              
                              (3,986,553
                              )TOTAL
      LIABILITIES AND EQUITY (DEFICIT)
                              
                              $
                              6,227,389
                              
                              
                              $
                              5,091,792
 
 The
accompanying notes are an integral part of these condensed consolidated
financial statements
  1
  GLOBAL
CLEAN ENERGY HOLDINGS, INC. AND SUBSIDIARIES
 (A
Development Stage Company)
 CONDENSED
CONSOLIDATED STATEMENTS OF OPERATIONS
 (Unaudited)
  From Inception ofthe Development StageFor the Three Months Ended
                                    
                                    
                                    on November 20, 1991March 31,
                                    
                                    
                                    through2009
                                    
                                    
                                    2008
                                    
                                    
                                    March 31, 2009Revenue
                                    
                                    $
                                    40,000
                                    
                                    
                                    $
                                    -
                                    
                                    
                                    $
                                    40,000Operating
      ExpensesGeneral
      and administrative
                                    
                                    
                                    341,093
                                    
                                    
                                    
                                    511,025
                                    
                                    
                                    
                                    10,070,378Research
      and development
                                    
                                    
                                    -
                                    
                                    
                                    
                                    -
                                    
                                    
                                    
                                    986,584341,093
                                    
                                    
                                    
                                    511,025
                                    
                                    
                                    
                                    11,056,962Loss
      from Operations
                                    
                                    
                                    (301,093
                                    )
                                    
                                    
                                    (511,025
                                    )
                                    
                                    
                                    (11,016,962
                                    )Other
      Income (Expenses)Unrealized
      gain on financial instrument
                                    
                                    
                                    -
                                    
                                    
                                    
                                    5,469
                                    
                                    
                                    
                                    4,722,632Interest
      income
                                    
                                    
                                    1
                                    
                                    
                                    
                                    3,863
                                    
                                    
                                    
                                    66,916Interest
      expense
                                    
                                    
                                    (81,509
                                    )
                                    
                                    
                                    (15,030
                                    )
                                    
                                    
                                    (1,553,528
                                    )Interest
      expense from amortization of discounton
      secured promissory note
                                    
                                    
                                    -
                                    
                                    
                                    
                                    -
                                    
                                    
                                    
                                    (286,369
                                    )Gain
      on debt restructuring
                                    
                                    
                                    -
                                    
                                    
                                    
                                    -
                                    
                                    
                                    
                                    2,524,787Other
      income
                                    
                                    
                                    -
                                    
                                    
                                    
                                    -
                                    
                                    
                                    
                                    906,485Total
      Other Income (Expenses)
                                    
                                    
                                    (81,508
                                    )
                                    
                                    
                                    (5,698
                                    )
                                    
                                    
                                    6,380,923Loss
      from Continuing Operations
                                    
                                    
                                    (382,601
                                    )
                                    
                                    
                                    (516,723
                                    )
                                    
                                    
                                    (4,636,039
                                    )Income
      (Loss) from Discontinued Operations
                                    
                                    
                                    160,748
                                    
                                    
                                    
                                    (253,310
                                    )
                                    
                                    
                                    (22,355,661
                                    )Net
      Loss
                                    
                                    
                                    (221,853
                                    )
                                    
                                    
                                    (770,033
                                    )
                                    
                                    
                                    (26,991,700
                                    )Less
      net loss attributable to the noncontrollinginterest
                                    
                                    
                                    (157,765
                                    )
                                    
                                    
                                    -
                                    
                                    
                                    
                                    (472,880
                                    )Net
      Loss attributable to Global Clean EnergyHoldings,
      Inc.
                                    
                                    
                                    (64,088
                                    )
                                    
                                    
                                    (770,033
                                    )
                                    
                                    
                                    (26,518,820
                                    )Preferred
      stock dividend from beneficialconversion
      feature
                                    
                                    
                                    -
                                    
                                    
                                    
                                    -
                                    
                                    
                                    
                                    (692,199
                                    )Net
      Loss Applicable to Common Shareholders
                                    
                                    $
                                    (64,088
                                    )
                                    
                                    $
                                    (770,033
                                    )
                                    
                                    $
                                    (27,211,019
                                    )Amounts
      attributable to Global Clean EnergyHoldings,
      Inc. common shareholders:Loss
      from Continuing Operations
                                    
                                    $
                                    (224,836
                                    )
                                    
                                    $
                                    (516,723
                                    )
                                    
                                    $
                                    (4,163,159
                                    )Income
      (Loss) from Discontinued Operations
                                    
                                    
                                    160,748
                                    
                                    
                                    
                                    (253,310
                                    )
                                    
                                    
                                    (22,355,661
                                    )Net
      Loss
                                    
                                    $
                                    (64,088
                                    )
                                    
                                    $
                                    (770,033
                                    )
                                    
                                    $
                                    (26,518,820
                                    )Basic
      and Diluted Loss per Common Share:Loss
      from Continuing Operations
                                    
                                    $
                                    (0.001
                                    )
                                    
                                    $
                                    (0.003
                                    )Income
      (Loss) from Discontinued Operations
                                    
                                    $
                                    0.001
                                    
                                    
                                    $
                                    (0.001
                                    )Net
      loss
                                    
                                    $
                                    (0.000
                                    )
                                    
                                    $
                                    (0.004
                                    )Basic
      and Diluted Weighted-Average CommonShares
      Outstanding
                                    
                                    
                                    224,813,819
                                    
                                    
                                    
                                    174,838,967
 
 The
accompanying notes are an integral part of these condensed consolidated
financial statements
  2
  GLOBAL
CLEAN ENERGY HOLDINGS, INC. AND SUBSIDIARIES
 (A
Development Stage Company)
 CONDENSED
CONSOLIDATED STATEMENTS OF CASH FLOWS
 (Unaudited)
  From Inception ofthe Development StageFor the Three Months Ended
                                    
                                    
                                    on November 20, 1991March 31,
                                    
                                    
                                    through2009
                                    
                                    
                                    2008
                                    
                                    
                                    March 31, 2009Cash
      Flows From Operating ActivitiesNet
      loss
                                    
                                    $
                                    (221,853
                                    )
                                    
                                    $
                                    (770,033
                                    )
                                    
                                    $
                                    (26,991,700
                                    )Adjustments
      to reconcile net loss to net cash used in operating
    activitiesForeign
      currency transaction loss (gain)
                                    
                                    
                                    (189,675
                                    )
                                    
                                    
                                    253,310
                                    
                                    
                                    
                                    60,347Gain
      on debt restructuring
                                    
                                    
                                    -
                                    
                                    
                                    
                                    -
                                    
                                    
                                    
                                    (2,524,787
                                    )Share-based
      compensation for services, expenses, litigation,and
      research and development
                                    
                                    
                                    59,884
                                    
                                    
                                    
                                    79,709
                                    
                                    
                                    
                                    12,774,064Commitment
      for research and development obligation
                                    
                                    
                                    -
                                    
                                    
                                    
                                    -
                                    
                                    
                                    
                                    2,378,445Depreciation
                                    
                                    
                                    549
                                    
                                    
                                    
                                    56
                                    
                                    
                                    
                                    139,580Reduction
      of escrow receivable from research and development
                                    
                                    
                                    -
                                    
                                    
                                    
                                    -
                                    
                                    
                                    
                                    272,700Unrealized
      loss (gain) on financial instrument
                                    
                                    
                                    -
                                    
                                    
                                    
                                    (5,469
                                    )
                                    
                                    
                                    (4,722,632
                                    )Interest
      expense from amortization of discount on securedpromissory
      note
                                    
                                    
                                    -
                                    
                                    
                                    
                                    -
                                    
                                    
                                    
                                    286,369Reduction
      of legal costs
                                    
                                    
                                    -
                                    
                                    
                                    
                                    -
                                    
                                    
                                    
                                    (130,000
                                    )Write-off
      of subscriptions receivable
                                    
                                    
                                    -
                                    
                                    
                                    
                                    -
                                    
                                    
                                    
                                    112,500Impairment
      loss on assets
                                    
                                    
                                    -
                                    
                                    
                                    
                                    -
                                    
                                    
                                    
                                    9,709Gain
      on disposal of assets, net of losses
                                    
                                    
                                    -
                                    
                                    
                                    
                                    -
                                    
                                    
                                    
                                    (228,445
                                    )Write-off
      of receivable
                                    
                                    
                                    -
                                    
                                    
                                    
                                    -
                                    
                                    
                                    
                                    562,240Note
      payable issued for litigation
                                    
                                    
                                    -
                                    
                                    
                                    
                                    -
                                    
                                    
                                    
                                    385,000Changes
      in operating assets and liabilitiesAccounts
      receivable
                                    
                                    
                                    (20,000
                                    )
                                    
                                    
                                    -
                                    
                                    
                                    
                                    (27,529
                                    )Other
      current assets
                                    
                                    
                                    5,217
                                    
                                    
                                    
                                    9,710
                                    
                                    
                                    
                                    (126,498
                                    )Accounts
      payable and accrued expenses
                                    
                                    
                                    350,620
                                    
                                    
                                    
                                    106,513
                                    
                                    
                                    
                                    5,370,946Net
      Cash Used in Operating Activities
                                    
                                    
                                    (15,258
                                    )
                                    
                                    
                                    (326,204
                                    )
                                    
                                    
                                    (12,399,691
                                    )Cash
      Flows From Investing ActivitiesPlantation
      development costs
                                    
                                    
                                    (487,661
                                    )
                                    
                                    
                                    (243,669
                                    )
                                    
                                    
                                    (2,584,354
                                    )Purchase
      of property and equipment
                                    
                                    
                                    -
                                    
                                    
                                    
                                    -
                                    
                                    
                                    
                                    (740,237
                                    )Proceeds
      from disposal of assets
                                    
                                    
                                    -
                                    
                                    
                                    
                                    -
                                    
                                    
                                    
                                    310,000Change
      in deposits
                                    
                                    
                                    -
                                    
                                    
                                    
                                    -
                                    
                                    
                                    
                                    (53,791
                                    )Issuance
      of note receivable
                                    
                                    
                                    -
                                    
                                    
                                    
                                    -
                                    
                                    
                                    
                                    (313,170
                                    )Payments
      received on note receivable
                                    
                                    
                                    -
                                    
                                    
                                    
                                    -
                                    
                                    
                                    
                                    130,000Net
      Cash Used in Investing Activities
                                    
                                    
                                    (487,661
                                    )
                                    
                                    
                                    (243,669
                                    )
                                    
                                    
                                    (3,251,552
                                    )Cash
      Flows From Financing ActivitiesProceeds
      from common stock, preferred stock, and warrants for cash
                                    
                                    
                                    -
                                    
                                    
                                    
                                    75,000
                                    
                                    
                                    
                                    11,424,580Proceeds
      from issuance of preferred membership in GCE Mexico I, LLC
                                    
                                    
                                    1,071,278
                                    
                                    
                                    
                                    -
                                    
                                    
                                    
                                    3,486,429Contributed
      equity
                                    
                                    
                                    -
                                    
                                    
                                    
                                    -
                                    
                                    
                                    
                                    131,374Proceeds
      from notes payable and related warrants
                                    
                                    
                                    15,000
                                    
                                    
                                    
                                    -
                                    
                                    
                                    
                                    1,961,613Payments
      on notes payable
                                    
                                    
                                    -
                                    
                                    
                                    
                                    (50,000
                                    )
                                    
                                    
                                    (951,287
                                    )Proceeds
      from convertible notes payable
                                    
                                    
                                    -
                                    
                                    
                                    
                                    -
                                    
                                    
                                    
                                    571,702Payments
      on convertible notes payable
                                    
                                    
                                    -
                                    
                                    
                                    
                                    -
                                    
                                    
                                    
                                    (98,500
                                    )Net
      Cash Provided by Financing Activities
                                    
                                    
                                    1,086,278
                                    
                                    
                                    
                                    25,000
                                    
                                    
                                    
                                    16,525,911Net
      Increase (Decrease) in Cash and Cash Equivalents
                                    
                                    
                                    583,359
                                    
                                    
                                    
                                    (544,873
                                    )
                                    
                                    
                                    874,668Cash
      and Cash Equivalents at Beginning of Period
                                    
                                    
                                    291,309
                                    
                                    
                                    
                                    805,338
                                    
                                    
                                    
                                    -Cash
      and Cash Equivalents at End of Period
                                    
                                    
                                    874,668
                                    
                                    
                                    
                                    260,465
                                    
                                    
                                    
                                    874,668Supplemental
      Disclosures of Cash Flow Information:Cash
      paid for interest
                                    
                                    $
                                    -
                                    
                                    
                                    $
                                    670Noncash
      Investing and Financing Activities:Reclassification
      of financial instrument to permanent equity
                                    
                                    $
                                    -
                                    
                                    
                                    $
                                    2,161,045Accrual
      of return on noncontrolling interest
                                    
                                    
                                    93,523
                                    
                                    
                                    
                                    -Plantation
      development costs financed by accounts payable
                                    
                                    
                                    50,383
                                    
                                    
                                    
                                    -Equipment
      depreciation capitalized to plantation development costs
                                    
                                    
                                    10,539
                                    
                                    
                                    
                                    -
 The
accompanying notes are an integral part of these condensed consolidated
financial statements
  3
  GLOBAL
CLEAN ENERGY HOLDINGS, INC. AND SUBSIDIARIES
 (A
Development Stage Company)
 Notes
to Unaudited Condensed Consolidated Financial Statements
  Note
1 –  History and Basis of Presentation
 
 History
 
 Medical
Discoveries, Inc. was incorporated under the laws of the State of Utah on
November 20, 1991. Effective as of August 6, 1992, the Company merged
with and into WPI Pharmaceutical, Inc., a Utah corporation (“WPI”), pursuant to
which WPI was the surviving corporation. Pursuant to the MDI-WPI merger, the
name of the surviving corporation was changed to Medical Discoveries, Inc.
(“MDI”).  MDI’s initial purpose was the research and development of an
anti-infection drug know as MDI-P.
 
 On
March 22, 2005, MDI formed MDI Oncology, Inc., a Delaware corporation, as a
wholly-owned subsidiary to acquire and operate the assets and business
associated with the Savetherapeutics transaction.  With this
transaction, MDI acquired the SaveCream technology and carried on the research
and development of this drug candidate.  As discussed in Note 9, MDI
made the decision in 2007 to discontinue further development of these two drug
candidates and sell these technologies.
 
 On
September 7, 2007, MDI entered into a share exchange agreement pursuant to which
it acquired all of the outstanding ownership interests in Global Clean Energy
Holdings, LLC, discussed further in Note 3.  Global Clean Energy
Holdings, LLC was an entity that had certain trade secrets, know-how, business
plans, term sheets, business relationships, and other information relating to
the start-up of a business related to the cultivation and production of seed oil
from the seed of the Jatropha plant.  With this transaction, MDI
commenced the research and development of a business whose purpose will be
providing feedstock oil intended for the production of bio-diesel.
 
 On
January 29, 2008, a meeting of shareholders was held and, among other things,
the name Medical Discoveries, Inc. was changed to Global Clean Energy Holdings,
Inc. (the “Company”).
 
 Effective
April 23, 2008, the Company entered into a limited liability company agreement
to form GCE Mexico I, LLC (GCE Mexico) along with six unaffiliated
investors.  The Company owns 50% of the common membership interest of
GCE Mexico and five of the unaffiliated investors own the other 50% of the
common membership interest.  Additionally, a total of 1,000 preferred
membership units were issued to two of the unaffiliated
investors.  GCE Mexico owns a 99% interest in Asideros Globales
Corporativo, (Asideros) a corporation newly organized under the laws of Mexico,
and the Company owns the remaining 1% directly.  Commencing in April
2008, the Company has consolidated the financial statements of GCE Mexico and
Asideros with its financial statements.  The ownership interests of
the six unaffiliated investors in GCE Mexico is presented as noncontrolling
interest in the accompanying consolidated financial statements.  GCE
Mexico was organized primarily to, among other things, acquire land in Mexico
through Asideros for the cultivation of the Jatropha plant.
 
 Unaudited Interim
Consolidated Financial Statements
 
 The
accompanying unaudited condensed consolidated financial statements have been
prepared by the Company pursuant to the rules and regulations of the Securities
and Exchange Commission. Certain information and footnote disclosures normally
included in financial statements prepared in accordance with accounting
principles generally accepted in the United States of America have been
condensed or omitted pursuant to such rules and regulations.  In the
opinion of management, all adjustments and disclosures necessary for a fair
presentation of these financial statements have been included and are of normal,
recurring nature.  These financial statements should be read in
conjunction with the financial statements and notes thereto included in the
Company’s annual report on Form 10-K for the year ended December 31, 2008, as
filed with the Securities and Exchange Commission.  The results of
operations for the three months ended March 31, 2009, may not be indicative of
the results that may be expected for the year ending December 31,
2009.
  4
 GLOBAL
CLEAN ENERGY HOLDINGS, INC. AND SUBSIDIARIES
 (A
Development Stage Company)
 Notes
to Unaudited Condensed Consolidated Financial Statements
 Loss per Common
Share
 
 Loss per
share amounts are computed by dividing loss applicable to the common
shareholders of the Company by the weighted-average number of common shares
outstanding during each period. Diluted loss per share amounts are computed
assuming the issuance of common stock for potentially dilutive common stock
equivalents.  All outstanding stock options, warrants, convertible
notes, convertible preferred stock, and common stock held in escrow are
currently antidilutive and have been excluded from the calculations of diluted
loss per share at March 31, 2009 and 2008, as follows:
 
 March 31,2009
                    
                    
                    2008Convertible
      notes
                    
                    
                    128,671
                    
                    
                    
                    128,671Convertible
      preferred stock - Series A
                    
                    
                    -
                    
                    
                    
                    57,856,000Convertible
      preferred stock - Series B
                    
                    
                    11,818,181
                    
                    
                    
                    11,818,181Warrants
                    
                    
                    29,742,552
                    
                    
                    
                    29,688,934Compensation-based
      stock options and warrants
                    
                    
                    52,159,083
                    
                    
                    
                    49,383,000Common
      stock held in escrow
                    
                    
                    4,567,519
                    
                    
                    
                    22,837,59398,416,006
                    
                    
                    
                    171,712,379
 
 Recently Issued Accounting
Standards
 
 In
December 2007, the FASB issued SFAS No. 141 (revised 2007), Business
Combinations (SFAS 141(R)), which replaces SFAS 141, Business
Combinations.  In April 2009, the Financial Accounting Standards Board
(FASB) issued FASB Staff Position (FSP) No. FAS 141(R)-1, Accounting
for Assets Acquired and Liabilities Assumed in a Business Combination That Arise
from Contingencies, which amends and clarifies the initial recognition and
measurement, subsequent measurement and accounting, and related disclosures of
assets and liabilities arising from contingencies in a business combination
under SFAS 141(R).  SFAS 141(R) and this FSP are effective for
business combinations for which the acquisition date is on or after
December 15, 2008. The adoption of these standards did not have any
immediate effect on our consolidated financial statements, however, the revised
standards will govern the accounting for any future business combinations that
we may enter into.
 
 In
September 2006, the FASB issued SFAS No. 157, Fair Value Measurements (SFAS
157), which defines fair value, establishes a framework for measuring fair value
in accordance with generally accepted accounting principles and expands
disclosures about fair value measurements. SFAS No. 157 was effective for
fiscal years beginning after November 15, 2007, and interim periods within
those fiscal years. In February 2008, FSP No. 157-2 delayed the
effective date of SFAS No. 157 one year for all nonfinancial assets and
nonfinancial liabilities, except those recognized or disclosed at fair value in
the financial statements on a recurring basis.  Those assets and
liabilities measured at fair value under SFAS No. 157 at January 1, 2008
did not have a material impact on our consolidated financial statements. The
adoption of FSP 157-2 for nonfinancial assets and liabilities at January 1, 2009
did not have a material impact on our consolidated financial
statements.
 
 In April
2009, the FASB issued FSP No. FAS 157-4, Determining Fair Value When the Volume
and Level of Activity for the Asset or Liability Have Significantly Decreased
and Identifying Transactions That Are Not Orderly, which provides additional
guidance for estimating fair value in accordance with SFAS No. 157. This
FSP states that a significant decrease in the volume and level of activity for
the asset or liability when compared with normal market activity is an
indication that transactions or quoted prices may not be determinative of fair
value because there may be increased instances of transactions that are not
orderly in such market conditions. Accordingly, further analysis of transactions
or quoted prices is needed, and a significant adjustment to the transactions or
quoted prices may be necessary to estimate fair value. This FSP is effective for
us beginning April 1, 2009. We do not expect the impact of the adoption of
this FSP to be material on our consolidated financial statements.
 5
 GLOBAL
CLEAN ENERGY HOLDINGS, INC. AND SUBSIDIARIES
 (A
Development Stage Company)
 Notes
to Unaudited Condensed Consolidated Financial
Statements
 In April
2009, the FASB issued FSP No. FAS 107-1 and APB 28-1, Interim Disclosures about
Fair Value of Financial Instruments, which requires disclosures about the fair
value of our financial instruments for which it is practicable to estimate that
value, whether recognized or not recognized in the balance sheets, in the
interim reporting periods as well as in the annual reporting periods. In
addition, the FSP requires disclosures of the methods and significant
assumptions used to estimate the fair value of those financial instruments. This
FSP is effective for us beginning April 1, 2009. We do not expect the
impact of the adoption of this FSP to be material on our consolidated financial
statements.
  In April
2009, the FASB issued FSP No. FAS 115-2 and FAS 124-2, Recognition and
Presentation of Other-Than-Temporary Impairments, which establishes a new method
of recognizing and reporting other-than-temporary impairments of debt securities
and requires additional disclosures related to debt and equity securities. This
FSP does not change existing recognition and measurement guidance related to
other-than-temporary impairments of equity securities. This FSP is effective for
us beginning April 1, 2009. We do not expect the impact of the adoption of
this FSP to be material on our consolidated financial statements.
 
 Note
2 –  Going Concern Considerations
 
 The
accompanying unaudited consolidated financial statements have been prepared
assuming that the Company will continue as a going concern.  The
Company incurred a net loss applicable to its common shareholders of $64,088 and
$1,707,562 during the three-month period ended March 31, 2009 and the year ended
December 31, 2008, respectively, and has incurred losses applicable to its
common shareholders since inception of the development stage of
$27,211,019.  The Company also used cash in operating activities of
$15,258 and $1,004,670 during the three-month period ended March 31, 2009 and
the year ended December 31, 2008, respectively.  At March 31, 2009,
the Company has negative working capital of $6,325,708 and a stockholders’
deficit attributable to its stockholders of $5,952,779.  These factors
raise substantial doubt about the Company’s ability to continue as a going
concern.
 
 The
Company discontinued its former bio-pharmaceutical business during the quarter
ended March 31, 2007.  Management plans to meet its cash needs through
various means including selling assets related to its former bio-pharmaceutical
business, securing financing, entering into joint ventures, and developing a new
business model.  In order to fund its new operations related to the
cultivation of the Jatropha plant, the Company sold Series B preferred stock
during the quarter ended December 31, 2007 in the amount of $1,300,000, issued a
secured promissory note under which the Company has borrowings of $475,000, and
has received $3,486,429 in capital contributions from the preferred membership
interest in GCE Mexico I, LLC. The Company is developing a new business
operation to participate in the rapidly growing bio-diesel
industry.  The Company continues to expect to be successful in this
new venture, but there is no assurance that its business plan will be
economically viable.  The ability of the Company to continue as a
going concern is dependent on that plan’s success. The financial statements do
not include any adjustments that might be necessary if the Company is unable to
continue as a going concern.
  6
 GLOBAL
CLEAN ENERGY HOLDINGS, INC. AND SUBSIDIARIES
 (A
Development Stage Company)
 Notes
to Unaudited Condensed Consolidated Financial Statements
 Note
3 –  Jatropha Business Venture
 
 Having
agreed to discontinue its bio-pharmaceutical operations and dispose of the
related assets, the Company considered entering into a number of other
businesses that would enable it to be able to provide the shareholders with
future value.  The Company’s Board of Directors decided to develop a
business to produce and sell seed oils, including seed oils harvested from the
planting and cultivation of the Jatropha curcas plant, for
the purpose of providing feedstock oil intended for the generation of methyl
ester, otherwise known as bio-diesel (the “Jatropha Business”).  The
Company’s Board concluded that there was a significant opportunity to
participate in the rapidly growing biofuels industry, which previously was
mainly driven by high priced, edible oil-based feedstock.  In order to
commence its new Jatropha Business, the Company entered into various
transactions during September and October of 2007, including: (i) hired Richard
Palmer, an energy consultant, and a member of Global Clean Energy Holdings LLC
(“Global”) to act as its new President, Chief Operating Officer and future Chief
Executive Officer, (ii) engaged Mobius Risk Group, LLC, a Texas company engaged
in providing energy risk advisory services, to provide it with consulting
services related to the development of the Jatropha Business, (iii) acquired
certain trade secrets, know-how, business plans, term sheets, business
relationships, and other information relating to the cultivation and production
of seed oil from the Jatropha plant for the production of bio-diesel from
Global, and (iv) engaged Corporativo LODEMO S.A DE CV to assist with the
development of the Jatropha Business in Mexico.  Subsequent to
entering into these transactions, the Company identified certain real property
in Mexico it believed to be suitable for cultivating the Jatropha
plant.  During April 2008, the Company entered into a limited
liability company agreement to form GCE Mexico I, LLC (GCE Mexico). In August
2008 the Company terminated the agreement with Mobius Risk Group, LLC. Through
Asideros Globales Corporativo (Asideros), a Mexican corporation of which GCE
Mexico holds a 99% equity interest and Global Clean Energy Holdings, Inc. holds
a 1% equity interest, land has been acquired in Mexico for the cultivation of
the Jatropha plant.  All of these transactions are described in
further detail in the remainder of this note to the consolidated financial
statements.
 
 Share Exchange
Agreement
 
 The
Company entered into a share exchange agreement (the Global Agreement) pursuant
to which the Company acquired all of the outstanding ownership interests in
Global Clean Energy Holdings, LLC, a Delaware limited liability company
(Global), on September 7, 2007 from Mobius Risk Group, LLC (Mobius) and from
Richard Palmer (Mr. Palmer).  Mr. Palmer owns a 13.33% equity interest
in Mobius and became the Company’s new President and Chief Operating Officer in
September 2007 and its Chief Executive Officer in December
2007.  Mobius and Mr. Palmer are considered related parties to the
Company.  Global is an entity that has certain trade secrets,
know-how, business plans, term sheets, business relationships, and other
information relating to the start-up of a business related to the cultivation
and production of seed oil from the seed of the Jatropha plant, for the purpose
of providing feedstock oil intended for the production of
bio-diesel.
 
 Mobius Consulting
Agreement
 
 Concurrent
with the execution of the Global Agreement, the Company entered into a
consulting agreement with Mobius pursuant to which Mobius agreed to provide
consulting services to the Company in connection with the Company’s new Jatropha
bio-diesel feedstock business. The Company engaged Mobius as a consultant to
obtain Mobius’ experience and expertise in the feedstock/bio-diesel market to
assist the Company and Mr. Palmer in developing this new line of operations for
the Company.  Mobius agreed to provide the following services to the
Company: (i) manage and supervise a contemplated research and development
program contracted by the Company and conducted by the University of Texas Pan
American regarding the location, characterization, and optimal economic
propagation of the Jatrophaplant; and (ii) assist
with the management and supervision of the planning, construction, and start-up
of plant nurseries and seed production plantations in Mexico, the Caribbean or
Central America.
  7
  GLOBAL
CLEAN ENERGY HOLDINGS, INC. AND SUBSIDIARIES
 (A
Development Stage Company)
 Notes
to Unaudited Condensed Consolidated Financial Statements
  The term
of the agreement was twelve months and the scope of work under the agreement was
completed in September 2008.  Mobius supervised the hiring of certain
staff to serve in management and operations roles of the Company, or hired such
persons to provide similar services as independent
contractors.  Mobius’ compensation for the services provided under the
agreement was a monthly retainer of $45,000.  The Company also
reimbursed Mobius for reasonable business expenses incurred in connection with
the services provided.  The agreement contained customary
confidentiality provisions with respect to any confidential information
disclosed to Mobius or which Mobius received while providing services under the
agreement.  Under this agreement, the Company has paid Mobius or
accrued $135,000 during the three months ended March 31, 2008, of which $13,500
was expensed as compensation to Mobius and $121,500 was capitalized as
plantation development costs pursuant to AICPA Statement of Position 85-3, Accounting by Agricultural Producers
and Agricultural Cooperatives.
 
 LODEMO
Agreement
 
 On
October 15, 2007, the Company entered into a service agreement with Corporativo
LODEMO S.A DE CV, a Mexican corporation (the LODEMO Group).  The
Company had decided to initiate its Jatropha Business in Mexico, and had
identified parcels of land in Mexico to plant and cultivate
Jatropha.  In order to obtain all of the logistical and other services
needed to operate a large-scale farming and transportation business in Mexico,
the Company entered into the service agreement with the LODEMO Group, a
privately held Mexican company with substantial land holdings, significant
experience in diesel distribution and sales, liquids transportation, logistics,
land development and agriculture.
 
 Under the
supervision of the Company’s management, the LODEMO Group is or will be
responsible for the establishment, development, and day-to-day operations of the
Jatropha Business in Mexico, including the extraction of the oil from the
Jatropha seeds, the delivery of the Jatropha oil to buyers, the purchase or
lease of land in Mexico, the establishment and operation of one or more Jatropha
nurseries, the clearing, planting and cultivation of the Jatropha fields, the
harvesting of the Jatropha seeds, the operation of the Company’s oil extraction
facilities, and the logistics associated with the foregoing.  Although
the LODEMO Group is responsible for identifying and acquiring the farmland,
ownership of the farmland or any lease thereto will be held directly by the
Company or by a Mexican subsidiary of the Company.  The LODEMO Group
will be responsible for hiring and managing all necessary
employees.  All direct and budgeted costs of the Jatropha Business in
Mexico will be borne by the Company.
 
 The
LODEMO Group provides the foregoing and other necessary services for a fee
primarily based on the number of hectares of Jatropha under
cultivation.  The Company has agreed to pay the LODEMO Group a fixed
fee per year of $60 per hectare of land planted and maintained with minimum
payments based on 10,000 hectares of developed land, to follow a planned
planting schedule. The Agreement has a 20-year term but may be terminated
earlier by the Company under certain circumstances.  The LODEMO Group
will also potentially receive incentive compensation for controlling costs below
the annual budget established by the parties, production incentives for
increased yield and a sales commission for biomass sales.  Under this
agreement, the Company has paid the LODEMO Group or accrued $462,320 and $91,529
during the three-month periods ended March 31, 2009 and 2008, respectively, all
of which was capitalized as plantation development costs pursuant to AICPA
Statement of Position 85-3, Accounting by Agricultural Producers
and Agricultural Cooperatives.  As of March 31, 2009, the
Company owed $50,343 of plantation development costs to the LODEMO
Group.  As of December 31, 2008, the Company had prepaid $98,159 of
plantation development costs to the LODEMO Group.
 
 8
  GLOBAL
CLEAN ENERGY HOLDINGS, INC. AND SUBSIDIARIES
 (A
Development Stage Company)
 Notes
to Unaudited Condensed Consolidated Financial Statements
  GCE Mexico I,
LLC
 
 Effective
April 23, 2008, the Company entered into a limited liability company agreement
(“LLC Agreement”) to form GCE Mexico I, LLC, a Delaware limited liability
company (GCE Mexico), with six unaffiliated investors (collectively, the
Investors).  GCE Mexico was organized primarily to acquire
approximately 5,000 acres of farm land (the Jatropha Farm) in the State of
Yucatan in Mexico to be used primarily for the (i) cultivation of Jatropha curcas, (ii) the
marketing and sale of the resulting fruit, seeds, or pre-processed crude
Jatropha oil, whether as biodiesel feedstock, biomass or otherwise, and (iii)
the sale of carbon value, green fuel value, or renewable energy credit value
(and other similar environmental attributes) derived from activities at the
Jatropha Farm.
 
 Under the
LLC Agreement, the Company owns 50% of the issued and outstanding common
membership units of GCE Mexico.  The remaining 50% of the common
membership units was issued to five of the Investors.  The Company and
the other owners of the common membership interest were not required to make
capital contributions to GCE Mexico.
 
 In
addition, two of the Investors agreed to invest in GCE Mexico through the
purchase of preferred membership units and through the funding of the purchase
of land in Mexico.  An aggregate of 1,000 preferred membership units
were issued to these two Investors who each agreed to make capital contributions
to GCE Mexico in installments and as required, to fund the development and
operations of the Jatropha Farm.  Total capital contributions of
$3,486,429 have been received by GCE Mexico from these Investors since the
execution of the LLC Agreement.  The LLC Agreement calls for
additional contributions from the Investors, as requested by management and as
required by the operation in 2009 and the following years.  These
Investors are entitled to earn a preferential 12% per annum cumulative
compounded return on the cumulative balance of their preferred membership
interest.
 
 These
investors also directly funded the purchase of approximately 5,000 acres of land
in the State of Yucatan in Mexico by the payment of $2,051,282.  The
land was acquired in the name of Asideros and Asideros issued a mortgage in the
amount of $2,051,282 in favor of these two Investors.  The mortgage
bears interest at the rate of 12% per annum, payable quarterly.  The
Board has directed that this interest shall continue to accrue until such time
as the Board determines that there is sufficient cash flow to pay all accrued
interest.  The entire mortgage, including any unpaid interest, is due
April 23, 2018.
 
 According
to the LLC Agreement, the net loss of GCE Mexico is allocated to the members
according to the investment balances.  Accordingly, since the common
membership interest did not make a capital contribution, all of the losses have
been allocated to the preferred membership interest.   The
noncontrolling interest presented in the accompanying consolidated balance sheet
includes the carrying value of the preferred membership interests and of the
common membership interests owned by the Investors, and excludes any common
membership interest in GCE Mexico held by the Company.
  9
 GLOBAL
CLEAN ENERGY HOLDINGS, INC. AND SUBSIDIARIES
 (A
Development Stage Company)
 Notes
to Unaudited Condensed Consolidated Financial Statements
 Note
4 –  Property and Equipment
 
 Property
and equipment are as follows:
 
 March 31,
                          
                          
                          December 31,2009
                          
                          
                          2008Land
                          
                          $
                          2,051,282
                          
                          
                          $
                          2,051,282Plantation
      development costs
                          
                          
                          2,665,604
                          
                          
                          
                          2,117,061Plantation
      equipment
                          
                          
                          509,037
                          
                          
                          
                          509,037Office
      equipment
                          
                          
                          10,993
                          
                          
                          
                          10,993Total
      cost
                          
                          
                          5,236,916
                          
                          
                          
                          4,688,373Less
      accumulated depreciation
                          
                          
                          (33,384
                          )
                          
                          
                          (22,296
                          )Property
      and equipment, net
                          
                          $
                          5,203,532
                          
                          
                          $
                          4,666,077
 
 The
Company has capitalized farming equipment and costs related to the development
of land for farm use in accordance with AICPA Statement of Position 85-3, Accounting by Agricultural Producers
and Agricultural Cooperatives.  Plantation equipment is
depreciated using the straight-line method over estimated useful lives of 5 to
15 years and is currently being capitalized as part of plantation development
costs.  Plantation development costs are not currently being
depreciated.  Upon completion of the plantation development,
development costs having a limited life and intermediate-life plants that have
growth and production cycles of more than one year will be depreciated over the
useful lives of the related assets.
 
 Commencing
in June 2008, GCE Mexico purchased certain equipment for purposes of rapidly
clearing the land, preparing the land for planting, and actually planting the
Jatropha trees.  The land, plantation development costs, and
plantation equipment are located in Mexico.
 
 Note
5 –  Accrued Payroll and Payroll Taxes
 
 Accrued
payroll and payroll taxes principally relate to unpaid compensation for officers
and directors that are no longer affiliated with the Company.  Accrued
payroll taxes will become due upon payment of the related accrued
compensation.  Accrued payroll and payroll taxes are composed of the
following:
 
 March 31,
                                
                                
                                December 31,2009
                                
                                
                                2008Former
      Chief Executive Officer, resigned 2007, including$500,000
      under the Release and Settlement Agreement
                                
                                $
                                570,949
                                
                                
                                $
                                570,949Other
      former Officers and Directors
                                
                                
                                311,200
                                
                                
                                
                                311,200Accrued
      payroll taxes on accrued compensation toformer
      officers and directors
                                
                                
                                38,510
                                
                                
                                
                                38,510Accrued
      payroll, vacation, and related payroll  taxesfor
      current officers
                                
                                
                                356,843
                                
                                
                                
                                238,149Accrued
      payroll and payroll taxes
                                
                                $
                                1,277,502
                                
                                
                                $
                                1,158,808
  10
 GLOBAL
CLEAN ENERGY HOLDINGS, INC. AND SUBSIDIARIES
 (A
Development Stage Company)
 Notes
to Unaudited Condensed Consolidated Financial Statements
 On August
31, 2007, the Company entered into a Release and Settlement Agreement with Judy
Robinett, the Company’s then-current Chief Executive Officer.  Under
the agreement, Ms. Robinett agreed to, among other things, assist the Company in
the sale of its legacy assets and complete the preparation and filing of the
delinquent reports to the Securities and Exchange Commission.  Under
the agreement, Ms. Robinett agreed to (i) forgive her potential right to receive
$1,851,805 in accrued and unpaid compensation, un-accrued and pro-rata bonuses,
and severance pay and (ii) the cancellation of stock options to purchase
14,000,000 shares of common stock at an exercise price of $0.02 per
share.  In consideration for her services, the forgiveness of the
foregoing cash payments, the cancellation of the stock options, and settlement
of other issues, the Company agreed to, among other things, to pay Ms. Robinett
$500,000 upon the receipt of the cash payment under the agreement to sell the
SaveCream Assets.  Pursuant to this agreement, Ms. Robinett resigned
on December 21, 2007.
 
 Note
6 –  Secured Promissory Note
 
 In order
to fund ongoing operations pending closing of the sale of the SaveCream Assets,
the Company entered into a loan agreement with, and issued a promissory note in
favor of, Mercator Momentum Fund III, L.P. (Mercator) in
September 2007.  At that time, Mercator, along with two other
affiliates, owned all of the issued and outstanding shares of the Company’s
Series A Convertible Preferred Stock.  Late in 2008, Mercator was
dissolved and the promissory note was distributed to the former limited partners
of Mercator.  During the three months ended March 31, 2009, the
noteholders agreed to extend the due date of the note to July 13, 2009 in
exchange for increasing the principal balance of the note by $15,000 and
increasing the interest rate by 2%.  At March 31, 2009, the principal
balance of the note is $475,000 and the note bears interest at
10.68%.  The loan is secured by a lien on all of the assets of the
Company.
 
 Note
7 –  Changes in Equity (Deficit)
 
 A summary
of the composition of Equity (Deficit) of the Company at March 31, 2009 and
2008, and the changes during the three months then ended is presented in the
following table:
 
 Total GlobalClean
                            Holdings,Inc.
                            stockholders'
                            equity (deficit)
                          
                          
                          Noncontrolling
                            interest
                          
                          
                          Total equity
                            (deficit)Balance
      at December 31, 2008
                          
                          $
                          (5,948,575
                          )
                          
                          $
                          1,962,022
                          
                          
                          $
                          (3,986,553
                          )Capital
      contribution from noncontrolling interest
                          
                          
                          -
                          
                          
                          
                          1,071,278
                          
                          
                          
                          1,071,278Share-based
      compensation
                          
                          
                          59,884
                          
                          
                          
                          -
                          
                          
                          
                          59,884Accrual
      of preferential return for the noncontrolling interest
                          
                          
                          -
                          
                          
                          
                          (93,523
                          )
                          
                          
                          (93,523
                          )Net
      loss
                          
                          
                          (64,088
                          )
                          
                          
                          (157,765
                          )
                          
                          
                          (221,853
                          )Balance
      at March 31, 2009
                          
                          $
                          (5,952,779
                          )
                          
                          $
                          2,782,012
                          
                          
                          $
                          (3,170,767
                          )
 
  Total GlobalClean
                          Holdings,Inc.
                          stockholders'
                          equity (deficit)
                        
                        
                        Noncontrolling
                          interest
                        
                        
                        Total equity
                          (deficit)Balance
      at December 31, 2007
                        
                        $
                        (7,034,431
                        )
                        
                        $
                        -
                        
                        
                        $
                        (7,034,431
                        )Reclassification
      of financial instrument to equity
                        
                        
                        2,161,045
                        
                        
                        
                        -
                        
                        
                        
                        2,161,045Share-based
      compensation
                        
                        
                        79,709
                        
                        
                        
                        -
                        
                        
                        
                        79,709Net
      loss
                        
                        
                        (770,033
                        )
                        
                        
                        -
                        
                        
                        
                        (770,033
                        )Balance
      at March 31, 2008
                        
                        $
                        (5,563,710
                        )
                        
                        $
                        -
                        
                        
                        $
                        (5,563,710
                        )
  11
 GLOBAL
CLEAN ENERGY HOLDINGS, INC. AND SUBSIDIARIES
 (A
Development Stage Company)
 Notes
to Unaudited Condensed Consolidated Financial Statements
 Prior to
January 29, 2008, the Company was unable to guarantee that there would be enough
shares of authorized common stock to settle certain “freestanding instruments”
arising from warrants attached to convertible preferred stock or other
sources.  Accordingly, the warrants were measured at their fair value
and recorded as a liability in the financial statements characterized as a
“Financial Instrument”.  As of January 29, 2008, the fair value of
this liability was recorded at $2,161,045.  On January 29, 2008, the
shareholders of the Company approved an increase in the number of authorized
shares of common stock from 250 million to 500 million.  Consequently,
as the result of this amendment to the Company’s Articles of Incorporation, the
Company was then able to settle all ‘freestanding
instruments”.  Accordingly, the Company reclassified the liability,
characterized in the financial statements as “Financial Instrument” to permanent
equity in January 2008.
 
 Note
8 – Stock Options and Warrants
 
 The
Company has two incentive stock option plans wherein 24,000,000 shares of
the Company’s common stock are reserved for issuance thereunder.  The
Company granted stock options during the three months ended March 31, 2008 to
acquire 4,500,000 million shares of the Company’s common stock to the new
Executive Vice-President and Chief Financial Officer.  No stock
options were granted during the three months eneded March 31,
2009.  No income tax benefit has been recognized for share-based
compensation arrangements.  The Company has recognized plantation
development costs totaling $124,565 related to a liability that was satisfied by
the issuance of warrants in 2008.  Otherwise, no share-based
compensation cost has been capitalized in the balance sheet.
 
 A summary
of the status of options and compensation-based warrants at March 31, 2009, and
changes during the three months then ended is presented in the following
table:
 
 WeightedWeighted
                            
                            AverageShares
                            
                            
                            Average
                            
                            Remaining
                            
                            AggregateUnder
                            
                            
                            Exercise
                            
                            Contractual
                            
                            IntrinsicOption
                            
                            
                            Price
                            
                            Life
                            
                            ValueOutstanding
      at December 31, 2008
                            
                            
                            52,159,083
                            
                            
                            $
                            0.03Granted
                            
                            
                            -
                            
                            
                            
                            -Expired
                            
                            
                            -
                            
                            
                            
                            -Outstanding
      at March 31, 2009
                            
                            
                            52,159,083
                            
                            
                            $
                            0.03
                            
                            6.2 years
                            
                            $
                            421,522Exercisable
      at March 31, 2009
                            
                            
                            36,309,083
                            
                            
                            $
                            0.03
                            
                            7.2 years
                            
                            $
                            421,522
 
 At March
31, 2009, options to acquire 80,000 shares of common stock have no stated
contractual life.  The fair value of other stock option grants and
compensation-based warrants is estimated on the date of grant or issuance using
the Black-Scholes option pricing model.  The weighted-average fair
value of stock options granted during the three months ended March 31, 2008 was
$0.042.  The weighted-average assumptions used for these options
granted during the three months ended March 31, 2008 were risk-free interest
rate of 2.4%, volatility of 127%, expected life of 5.2 years, and dividend yield
of zero.  The assumptions employed in the Black-Scholes option pricing
model include the following.  The expected life of stock options
represents the period of time that the stock options granted are expected to be
outstanding prior to exercise. The expected volatility is based on the
historical price volatility of the Company’s common stock. The risk-free
interest rate represents the U.S. Treasury constant maturities rate for the
expected life of the related stock options. The dividend yield represents
anticipated cash dividends to be paid over the expected life of the stock
options.
  12
 GLOBAL
CLEAN ENERGY HOLDINGS, INC. AND SUBSIDIARIES
 (A
Development Stage Company)
 Notes
to Unaudited Condensed Consolidated Financial Statements
 Share-based
compensation from all sources recorded during the three months ended March 31,
2009 and 2008 were $59,884 and $79,709, respectively, and is included in general
and administrative expense.  As of March 31, 2009, there is
approximately $235,000 of unrecognized compensation cost related to stock-based
payments that will be recognized over a weighted average period of approximately
1.4 years.  As further discussed in Note 10, in April 2009, the board
of directors approved the modification of the provisions of certain options and
of certain common stock held in escrow.  These modifications will
accelerate the vesting of the affected options and accelerate the release of the
affected common stock held in escrow, which will result in a new measurement of
share-based compensation and will accelerate the recognition of that
compensation in the financial statements of the Company.
 
 Stock
Warrants
 
 A summary
of the status of the warrants outstanding at March 31, 2009, and changes during
the three months then ended is presented in the following table:
 
 WeightedShares
                        
                        
                        AverageUnder
                        
                        
                        ExerciseWarrant
                        
                        
                        PriceOutstanding
      at December 31, 2008
                        
                        
                        29,742,552
                        
                        
                        $
                        0.01Issued
                        
                        
                        -
                        
                        
                        
                        -Expired
                        
                        
                        -
                        
                        
                        
                        -Outstanding
      at March 31, 2009
                        
                        
                        29,742,552
                        
                        
                        $
                        0.01
 
 Note
9 – Discontinued Operations
 
 Prior to
2007, the Company was a developmental-stage bio-pharmaceutical company engaged
in the research, validation, development and ultimate commercialization of two
drugs known as MDI-P and SaveCream.  The Board evaluated the value of
its developmental stage drug candidates and in March 2007, the Board determined
that the best course of action was to discontinue further development of these
drug candidates and sell these technologies.  MDI-P was a drug
candidate being developed as an anti-infective treatment for bacterial
infections, viral infections and fungal infections.  In August 2007,
the Company sold the MDI-P related assets.
 
 SaveCream
is a drug candidate that the Company was developing to reduce breast cancer
tumors.  From March of 2007 through July of 2008, the Company entered
into various agreements with Eucodis Pharmaceuticals Forschungs und Entwicklungs
GmbH, an Austrian company (Eucodis) related to the sale of the SaveCream
assets.  Eucodis entered into a binding letter of intent in March 2007
and later entered into a sale and purchase agreement in July
2007.  The sale and purchase agreement was approved by the Company’s
shareholders in January 2008.  Ultimately, all discussions and
agreements with Eucodis were terminated in July 2008 due to their inability to
obtain their own financing and their failure to close the
sale.  However, the principal officer of Eucodis has agreed to
continue to work with the Company in connection with the sale of the Company’s
legacy assets.
 
 The
Company has engaged investment banking firms to expedite the sale of the
SaveCream asset.  The Company continues to seek interested parties
that may purchase the asset.  However, the recent contraction of the
capital markets has negatively impacted the abilities for several potential
purchasers to consummate a purchase.  Although, management is
continuing to take steps to market and sell the SaveCream assets to potential
buyers, no assurance can be given that this sale will actually be completed in
the near future, or ever. Due to the inability of the investment bankers to
facilitate a sales transaction of the asset, the Company has terminated the
engagement of the investment banking firms.
  13
 GLOBAL
CLEAN ENERGY HOLDINGS, INC. AND SUBSIDIARIES
 (A
Development Stage Company)
 Notes
to Unaudited Condensed Consolidated Financial Statements
 Pursuant
to accounting rules for discontinued operations, the Company has classified all
revenue and expense related to the operations, assets, and liabilities of its
bio-pharmaceutical business as discontinued operations.  For all
periods prior to March 2007, the Company has reclassified all revenue and
operating expenses to discontinued operations, except for estimated general
corporate overhead, because all of its operations related to the discontinued
technologies.  For the three months ended March 31, 2009 and 2008, the
Income (Loss) from Discontinued Operations principally consists of foreign
currency transaction gains and losses related to current liabilities associated
with the discontinued operations that are denominated in euros.  The
Company has not recorded any gain or loss through March 31, 2009 associated with
the planned sale of the SaveCream assets.
 
 Note
10 –  Subsequent Events
 
 Acquisition of Jatropha Farm
in Belize
 
 On
October 29, 2008, the Company entered into a Stock Purchase Agreement with the
four shareholders of Technology Alternatives Limited (TAL), a company formed
under the Laws of Belize. TAL owns and operates a 400 acre farm in subtropical
Belize, Central America, that currently is producing Jatropha. TAL has also been
performing plant science research and has been providing technical advisory
services for propagation of Jatropha for a number of years.
 
 The
shareholders of TAL are unaffiliated persons residing in the United Kingdom.
Pursuant to the Stock Purchase Agreement, the Company will acquire 100% of the
issued and outstanding shares of TAL for common stock in the Company, thereby
making TAL a wholly-owned subsidiary of the Company. It is anticipated that the
Company will issue 8,952,756 common shares in exchange for all of the
outstanding shares of TAL. In addition to receiving the Company’s shares, the
sellers will be repaid the promissory notes previously issued to them by TAL.
However, as of March 31, 2009 all conditions precedent required for the exchange
of consideration had not been satisfied, and shares have not been issued.
Consequently, this transaction is not reflected in the Company’s financial
statements dated as of March 31, 2009.
 
 Furthermore,
the seller had an obligation to maintain the asset in accordance with the Stock
Purchase Agreement and failed to do so. Therefore, the sellers have agreed to
decrease the acquisition price and to decrease the principal amounts of the
promissory notes.
 
 The
selling shareholders had previously made loans to TAL to fund the operations of
TAL. As of October 29, 2008 the transaction contemplated by the Stock Purchase
Agreement, the remaining outstanding balance of these loans, in the aggregate,
was determined to be $453,611. To reflect the current value of TAL, these notes
will be reduced to $303,611 at closing. At the closing, the promissory notes
evidencing these loans will be replaced by new promissory notes issued by TAL to
the selling shareholders. The new notes have the following terms: (i) Interest
free for 90 days; (ii) Interest accrues at an annual rate of 8% per annum
commencing on the 91st day after the issuance of the notes; (iii) Interest
accrues until maturity; (iv) The entire remaining unpaid balance of the notes is
due and payable six months following the consumation of the transaction; (v) TAL
and/or the Company may prepay the notes at any time without penalty, and the
Company is required to prepay the notes if and when it receives future funding
in an amount that, in the Company’s reasonable discretion, is sufficient to
permit the prepayment of the notes without adversely affecting the Company’s
operations or financial condition. The new notes are secured by the deed of
legal mortgage on the 400 acre farm owned by TAL. Accordingly, in the event that
TAL defaults under the notes, the selling shareholders will have the right to
foreclose on the 400 acre Jatropha farm.
  14
 GLOBAL
CLEAN ENERGY HOLDINGS, INC. AND SUBSIDIARIES
 (A
Development Stage Company)
 Notes
to Unaudited Condensed Consolidated Financial Statements
 The
acquisition will be accounted for under the purchase method of accounting and
the results of operations of TAL will be consolidated with the results of
operations of the Company from the date of acquisition.
  Modification of Director and
Officer Compensation
 
 Effective
April 22, 2009, the Board of Directors approved the following changes in
compensation for the members of the board of directors and for the executive
officers:
 
 ·
              Compensation
      of $2,000 per month for each of the three non-employee members of the
      Board of Directors, commencing July 1,
2009.
 
 ·
              Options
      will be granted to each non-employee member of the Board of Directors to
      purchase 500,000 shares of the Company’s common stock commencing July 1,
      2009 and annually thereafter on July 1 of each successive
      year.  The exercise price of the options will be at fair market
      value, as determined by the closing price of the Company’s common stock on
      the day prior to the grant.  The options will have a term of
      five years until expiration.  The options will vest and become
      exercisable in ten equal monthly installments commencing on the month
      after the date of grant.
 
 ·
              Approved
      the release of 652,503 shares of common stock to Richard Palmer, the
      Company’s Chief Executive Officer.  These shares were previously
      part of the shares from the share exchange agreement to acquire Global
      Clean Energy Holdings, LLC in September 2007 that were being held in
      escrow pending the achievement of certain market-related
      milestones.  Mr. Palmer was also awarded the immediate vesting
      of options to purchase twelve million shares of the Company’s common stock
      previously granted.  These options were originally granted under
      the employment agreement with Mr. Palmer in September 2007 with vesting
      originally contingent upon the achievement of certain
      market-capitalization milestones.  The exercise price of these
      options remained unchanged at $0.03 per share and the term remained
      unchanged at five years from the date of
  employment.
 
 ·
              Approved
      the immediate vesting of options to purchase 2.5 million shares of the
      Company’s common stock held by Bruce Nelson, the Company’s Chief Financial
      Officer.  These options were originally granted under the
      employment agreement with Mr. Nelson in March 2008 with vesting originally
      contingent upon the achievement of certain market-capitalization
      milestones.  The exercise price of these options remained
      unchanged at $0.05 per share and the term remained unchanged at five years
      from the date of employment.
 
 ·
              Approved
      the immediate vesting of options to purchase an additional one million
      shares of the Company’s common stock held by Mr. Nelson.  These
      options were originally granted under the employment agreement with Mr.
      Nelson in March 2008 with vesting scheduled for June 2009 through March
      2010.  The exercise price of these options was changed to $0.05
      per share and the term remained unchanged at five years from the date of
      employment.




15





ITEM 2.   MANAGEMENTS’ DISCUSSION AND ANALYSIS
OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS.




This Report, including any documents
which may be incorporated by reference into this Report, contains
“Forward-Looking Statements” within the meaning of Section 27A of the Securities
Act of 1933, as amended, and Section 21E of the Securities Exchange Act of 1934,
as amended. All statements other than statements of historical fact are
“Forward-Looking Statements” for purposes of these provisions, including our
plans to cultivate, produce and market non-food based feedstock for applications
in the biofuels market, any projections of revenues or other financial items,
any statements of the plans and objectives of management for future operations,
any statements concerning the proposed sale of our legacy medical asset, any
statements concerning proposed new products or services, any statements
regarding future economic conditions or performance, and any statements of
assumptions underlying any of the foregoing. All Forward-Looking Statements
included in this document are made as of the date hereof and are based on
information available to us as of such date. We assume no obligation to update
any Forward-Looking Statement. In some cases, Forward-Looking Statements can be
identified by the use of terminology such as “may,” “will,” “expects,” “plans,”
“anticipates,” “intends,” “believes,” “estimates,” “potential,” or “continue,”
or the negative thereof or other comparable terminology. Although we believe
that the expectations reflected in the Forward-Looking Statements contained
herein are reasonable, there can be no assurance that such expectations or any
of the Forward-Looking Statements will prove to be correct, and actual results
could differ materially from those projected or assumed in the Forward-Looking
Statements. Future financial condition and results of operations, as well as any
Forward-Looking Statements are subject to inherent risks and uncertainties,
including any other factors referred to in our press releases and reports filed
with the Securities and Exchange Commission. All subsequent Forward-Looking
Statements attributable to the company or persons acting on its behalf are
expressly qualified in their entirety by these cautionary statements. Additional
factors that may have a direct bearing on our operating results are described
under “Risk Factors” and elsewhere in this report.




Introductory
Comment




Throughout
this Quarterly Report on Form 10-Q, the terms “we,” “us,” “our,” “our
company,” and “Company” refer to Global Clean Energy Holdings, Inc., a Utah
corporation, and, unless the context indicates otherwise, also includes the
following subsidiaries: (i) MDI Oncology, Inc., a Delaware corporation, (ii)
Global Clean Energy Holdings LLC, a Delaware limited liability company, (iii)
GCE Mexico I, LLC, a Delaware limited liability company, and (iv) Asideros
Globales Corporativo, a corporation organized under the laws of
Mexico.




Overview




Prior to
2007, Global Clean Energy Holdings, Inc. was a developmental-stage
bio-pharmaceutical company, known as Medical Discoveries, Inc., that was engaged
in the research, validation and development of two drugs. As more fully
described in this report, during 2007 our Board of Directors determined that we
could no longer fund the development of our two drug candidates and could not
obtain additional funding for these drug candidates. Accordingly, the Board
decided to sell our two drug candidates and to develop a new business in the
rapidly expanding business of renewable alternative energy sources. As a result,
our future business plan, and our current principal business activities include
the planting, cultivation, harvesting and processing of inedible plant feedstock
to generate seed oils and biomass for use in the biofuels industry, including
the production of bio-diesel.


16


Organizational
History




This
company was incorporated under the laws of the State of Utah on November 20,
1991. Effective as of August 6, 1992, this company merged with and into WPI
Pharmaceutical, Inc., a Utah corporation. Pursuant to merger, the name of this
company was changed to Medical Discoveries, Inc. WPI was incorporated under the
laws of the State of Utah on February 22, 1984 under the name Westport
Pharmaceutical, Inc. On January 29, 2008, our shareholders approved the change
of our corporate name, and on that date we amended our name to “Global Clean
Energy Holdings, Inc.” to reflect our new focus on the bio-diesel alternative
energy market.




On March
22, 2005, we formed MDI Oncology, Inc., a Delaware corporation, as a wholly
owned subsidiary to acquire certain breast cancer intellectual property assets
from the liquidation estate of Savetherapeutics, A.G.




Transition
to new Business




Until
2007, we were a developmental-stage bio-pharmaceutical company engaged in the
research, validation, and development of two drugs we referred to as MDI-P and
SaveCream. Both of these drugs were under development, and had not been approved
by the U.S. Food and Drug Administration (FDA). The total cost to develop these
two drugs, and to receive the approval from the FDA, would have cost many
millions of dollars and taken many more years.




Early in
2007, our Board of Directors determined that we could no longer fund the
development of our two drug candidates and that we could not obtain additional
funding for these drug candidates. Our Board also evaluated the value of the
SaveCream drug candidate that was being co-developed with Eucodis
Pharmaceuticals Forschungs – und Entwicklungs GmbH, an Austrian company later
known as Eucodis Pharmaceuticals GmbH (“Eucodis”), and the return we could
expect for our shareholders, and determined that the highest value for this drug
candidate could be realized through a sale of that drug candidate to Eucodis.
Accordingly, our Board sought to maximize the return from these assets through
their sale.




On July
6, 2007, we entered into an agreement with Eucodis to sell SaveCream, and on
January 29, 2008, our shareholders approved the sale of the SaveCream asset to
Eucodis. However, Eucodis was unable to complete the purchase of the assets, and
our agreement to sell the SaveCream assets to Eucodis expired. We are currently
still trying to sell our SaveCream technologies and other medical technologies.
We have engaged the services of an investment-banking firm to assist us in this
sales effort.




Having
decided to dispose of the foregoing assets, our Board decided to develop a
business in the alternative energy market as a producer of biofuels.
Accordingly, our new goal is to produce and sell seed oils, including seeds oils
harvested from the planting and cultivation of Jatropha curcas plant, for
the purpose of providing feedstock oil used for the generation of methyl ester,
otherwise known as bio-diesel (the “Jatropha Business”). In connection with
commencing our new Jatropha Business, effective September 7, 2007, we (i) hired
Richard Palmer, an energy consultant, and a member of Global Clean Energy
Holdings LLC (“Global LLC”) to act as the our new President, Chief Operating
Officer and future Chief Executive Officer, (ii) engaged Mobius Risk Group, LLC,
a Texas company engaged in providing energy risk advisory services, to provide
us with consulting services related to the development of the Jatropha Business,
and (iii) acquired certain trade secrets, know-how, business plans, term sheets,
business relationships, and other information relating to the cultivation and
production of seed oil from the Jatropha plant for the production of bio-diesel
from Global LLC.


17


Effective
April 23, 2008, we entered into a limited liability company agreement (“LLC
Agreement”) for GCE Mexico I, LLC, a Delaware limited liability company (“GCE
Mexico”), with six other unaffiliated persons (collectively, “Unaffiliated
Members”).  GCE Mexico was organized primarily to acquire
approximately 5,000 acres of farm land (the “Jatropha Farm”) in the State of
Yucatan in Mexico to be used primarily for the (i) cultivation of Jatropha curcas , (ii) the
marketing and sale of the resulting fruit, seeds, or pre-processed crude
Jatropha oil, whether as biodiesel feedstock, biomass or otherwise, and (iii)
the sale of carbon value, green fuel value, or renewable energy credit value
(and other similar environmental attributes) derived from activities at the
Jatropha Farm.




Under the
LLC Agreement, we own 50% of the issued and outstanding common membership units
of GCE Mexico. The remaining 50% in common membership units were issued to the
Unaffiliated Members. In addition, an aggregate of 1,000 preferred membership
units were issued to two Unaffiliated Members (“Preferred Members”) who have,
through March 31, 2009, contributed $3,486,429 to the capital of the GCE
Mexico.  The Preferred Members are entitled to earn a preferential 12%
per annum cumulative compounded return on the balance of their preferred
membership interest.  The capital contributions have been used to fund
the development and operations of the Jatropha Farm. We are not required to make
capital contributions to GCE Mexico.





Critical
Accounting Policies




The
preparation of financial statements in conformity with accounting principles
generally accepted in the United States require management to make estimates and
assumptions that affect the reported assets, liabilities, sales and expenses in
the accompanying financial statements. Critical accounting policies are those
that require the most subjective and complex judgments, often employing the use
of estimates about the effect of matters that are inherently uncertain. We are a
development stage company as defined by the Financial Accounting Standards
Board’s (“FASB”) Statement of Financial Accounting Standards (“SFAS”) No. 7,
“Accounting and Reporting by Development Stage Enterprises.” Accordingly, all
losses accumulated since inception have been considered as part of our
development stage activities. Certain other critical accounting policies,
including the assumptions and judgments underlying them, are disclosed in the
Note A to the Consolidated Financial Statements included in our annual report on
Form 10-K filed for the fiscal year ended December 31, 2008. However, we do not
believe that there are any alternative methods of accounting for our operations
that would have a material affect on our financial statements.


18


Results
Of Operations





In 2007 the Board of Directors
determined to discontinue our prior bio-pharmaceutical
operations.  Pursuant to accounting rules for discontinued operations,
we have classified all revenue and expense, except general corporate overhead,
for 2009, 2008 and prior periods related to the operations of our
bio-pharmaceutical business as discontinued operations.





Revenues and Gross
Profit.  We are still a development stage company and have not
had significant revenues from our operations or reached the level of our planned
operations.  We discontinued our prior bio-pharmaceutical operations
in March 2007.  In September 2007, we commenced operations in our new
bio-fuels Jatropha business, but we are still in the pre-development
agricultural stage of our operations and, therefore, do not anticipate
generating significant revenues from the sale of bio-fuel products until late
2009.  During the three months ended March 31, 2009, we recognized
revenue of $40,000 under a bio-fuel consulting services agreement.  We
did not recognize any revenues during the three months ended March 31,
2008.  We are, however, attempting to generate cash from the forward
sale of carbon credits, the sale of future oil delivery contracts, the sale of
some Jatropha seeds for seed propagation purposes, and by providing additional
bio-fuel consulting services.





Operating Expenses. Our
general and administrative expenses related to our continuing operations for the
three months ended March 31, 2009, were $341,000 compared to $511,000 for the
three months ended March 31, 2008.  General and administrative expense
principally includes officer compensation; outside services, such as legal,
accounting, and consulting expenses; share-based compensation; and other general
expenses such as insurance, occupancy costs, travel, etc.  The net
reduction in general and administrative expenses was $170,000 and was
principally the result of a reduction of $139,000 for the cost of outside
services for legal, accounting, and consulting services, and a reduction in
share-based compensation by $20,000.





Other Income/ Expense.
Interest expense increased from $15,000 for the three months ended March 31,
2008 to $82,000 for the three months ended March 31, 2009.  The
increase in interest expense is primarily attributable to interest on a mortgage
on land purchased in Mexico during April 2008.  The mortgage is in the
amount of $2,051,000 and accrues interest at the rate of 12% per
year.





During
the year ended December 31, 2008, we recorded $5,000 as unrealized gain on
financial instrument to record the accounting for and revaluation of certain
warrants previously classified as a liability in the financial
statements.  On January 29, 2008, our shareholders approved an
increase in the number of authorized shares of our common stock, resulting in
the reclassification of this financial instrument from liability to permanent
equity, and eliminated the requirement to periodically revalue the financial
instrument and recognize gain or loss on the revaluation.





Income (Loss) from Discontinued
Operations.  During the three months ended March 31, 2009, we
recognized income from discontinued operations of $161,000, compared to a loss
from discontinued operations $253,000 for the three months ended March 31,
2008.  The income or loss from discontinued operations for the three
months ended March 31, 2009 and 2008 principally relates to foreign currency
exchange rate gains or losses on liabilities associated with our former business
that are denominated in euros.





Net loss attributable to the
noncontrolling interest.  Effective April 23, 2008, we entered
into a limited liability company agreement (“LLC Agreement”) to form GCE Mexico
I, LLC, a Delaware limited liability company (GCE Mexico), with
six  unaffiliated investors (collectively, the
“Investors”).  Two of the Investors have invested $3,486,000 to
purchase GCE LLC preferred membership units.  An aggregate of 1,000
preferred membership units were issued to these two Investors.  Under
the LLC Agreement, the net loss of GCE Mexico is allocated to the members
according to the investment balances.  Accordingly, since the common
membership interest did not make a capital contribution, all of the losses have
been allocated to the preferred membership interest.   The net
loss attributable to the noncontrolling interest in the accompanying
Consolidated Statement of Operations represents the allocation of the net loss
of GCE Mexico I, LLC to the preferred membership interests.


19


Liquidity And Capital
Resources




As of
March 31, 2009, we had $874,668 in cash and had a working capital deficit of
$6,325,708 Since our inception, we have financed our operations primarily
through private sales of equity and debt financing. In order to fund our
short-term working capital needs, we will have to obtain additional
funding.  Virtually all of the cash reflected on our balance sheet is
reserved for the operation of GCE Mexico and our Jatropha
Farm.  Accordingly, most of those funds are not available to fund our
general and administrative or other operating expenses.




Our
ability to fund our liquidity and working capital needs will be dependent upon
certain potential transactions.  As previously disclosed, the
principal transaction that was expected to provide us with working capital was
the sale of SaveCream, our remaining legacy pharmaceutical assets.  In
2007 and again in 2008, we entered into two agreements with Eucodis
Pharmaceuticals GmbH (“Eucodis”) pursuant to which we agreed to sell our
SaveCream asset to Eucodis for an aggregate of €4,007,534 (or approximately U.S.
$6,331,503 based on the currency conversion rate in effect as of June 30,
2008).  The closing of the sale to Eucodis was initially scheduled to
occur in January 2008 and then again in April 2008. Unfortunately, Eucodis
declared bankruptcy, the closing did not occur, and all discussions and
agreements to sell the SaveCream assets to Eucodis were
terminated.  Accordingly, we have again commenced marketing that
asset.  However, as of the date of this filing, we have not found a
buyer for this medical asset, and no assurance can be given if or when we will
be able to dispose of our remaining legacy asset.  As previously
disclosed, the sale of the SaveCream asset would have eliminated many of our
outstanding liabilities and would have provided us with more than $2 million of
working capital.  As a result, the failure to sell our SaveCream asset
has severely and negatively affected our liquidity.





In order
to fund ongoing operations, in September 2007 we entered into a short-term loan
agreement with Mercator Momentum Fund III, L.P.
(“Mercator”).  Pursuant to the loan agreement, Mercator advanced
$350,000 to the Company, of which $200,000 remained outstanding and payable in
May 2008.   Interest under the loan agreement was payable on the
loan at a rate of 12% per annum. On May 19, 2008, the loan agreement was
modified to accrue interest at an interest rate of 8.68% per annum, Mercator
advanced an additional $250,000, and the amount available under that facility
was changed to $450,000.  In connection with this amendment Mercator
was granted a new warrant to purchase 581,395 shares of common stock (calculated
by dividing $75,000 by 130% of the closing price of the stock when exercised) at
a price of $0.129 per share.  Extensions to the maturity of this loan
were granted to the Company in August, October and November of 2008 and January
of 2009.  Mercator has dissolved and distributed the loan to its
limited partners who currently control the loan.  The loan is now
scheduled to mature on July 13, 2009.  The Company has agreed to
increase the principal amount of the note to $475,000 as consideration for the
granting of the extension of the maturity date.  This loan is secured
by a first priority lien on all of our assets.  Accordingly, in the
event that this loan in not repaid by its maturity date on July 13, 2009, or if
the current holders of the promissory note evidencing the loan do not agree to
extend the maturity date of this loan past the new maturity date, the holders of
the note will have the right to foreclose on all of our assets, which would have
a material adverse affect on our ability to continue our business plan and which
may result in the closure of our operations.





To date,
we have funded our operations from loans obtained from Mercator, from the
proceeds of the sale of the $1,300,000 of Series B Convertible Preferred Stock
in November 2007, and from management fees we have received from CGE Mexico I,
LLC and other clients.  However, we do not have sufficient cash to
continue our current operations and will need to raise funds in the immediate
future in order to continue to operate.





Our
business plan calls for significant infusion of additional capital to establish
additional Jatropha farms in Mexico and other locations. Because of our negative
working capital position, we currently do not have the funds necessary to
acquire and cultivate additional farms.  Accordingly, we will have to
obtain significant additional capital through the sale of equity and/or debt
securities, the forward sale of Jatropha oil and carbon offset credits, and from
other financing activities, such as strategic partnerships and joint ventures.
The formation and funding of the GCE Mexico I, LLC (previous called GCE LLC), as
previously discussed, is the first of a series of planned transactions to expand
our Jatropha operations.  The pending acquisition of a 400 acre
Jatropha farm in Belize  is the second step in the planned expansion
of the Company’s Jatropha plantations.  While we have commenced
negotiations with various third parties to obtain additional funding from
strategic partnerships and for the sale of carbon credits, no assurance can be
given that we will be able to enter into any agreements to obtain funding, sell
carbon credits or form additional strategic partnerships.  Without
raising additional cash (through the sale of our securities, the sale or carbon
credits, or strategic arrangements), we will not be able to effect our new
business plan in the Jatropha business and will have to further reduce our
operations, revise our business plan, and either/or temporarily or permanently
cease operations.


20





On April
29, 2008, we formed a new limited liability company, GCE Mexico I, LLC, that was
funded with a $2,051,282 million loan to acquire approximately 5,000 acres of
Jatropha farm land in Mexico.  Operating and development funds of
$957,271 (net of transaction costs) were also received by GCE Mexico I, LLC and
were used to develop the Jatropha Farm.  GCE Mexico’s limited partners
have contributed a total of $3,486,429to GCE Mexico I, LLC
through March 31, 2009.  As the owner of common membership interests,
the Company is not required to make any capital contributions to GCE Mexico I,
LLC.





On
October 29, 2008, we entered into a Stock Purchase Agreement with the four
shareholders of Technology Alternatives Limited, a company formed under the laws
of Belize (“TAL”), pursuant to which we agreed to purchase  all of the
issued and outstanding shares of TAL.  TAL owns and operates a 400
acre farm in subtropical Belize, Central America, that currently is producing
Jatropha.  TAL also has been performing plant science research and has
been providing technical advisory services for propagation of Jatropha for a
number of years.  The purchase of TAL has not yet been completed, but
is expected to be completed in the near future.  Under the Stock
Purchase Agreement, as amended, in consideration for the purchase of all of the
shares of TAL, we will have to deliver to the sellers at the
closing  (i) promissory notes in the aggregate amount of US $303,611,
and (ii) an aggregate of 8,952,756 unregistered shares of our common
stock.  The entire outstanding balance of the foregoing US $303,611 is
expected to mature six months following the consummation of the
transaction.  We currently do not have the funds to pay the full
amount of the promissory note that we will be required to deliver to the sellers
of TAL.  Since the TAL promissory notes will be secured by a mortgage
on the 400 acre farm, our failure to pay this note upon its maturity could
result in the loss of that farm and our investment in the Belizean Jatropha
farm.




Inflation
and changing prices have had no effect on our continuing operations over our two
most recent fiscal years.




We have
no off-balance sheet arrangements as defined in Item 303(a)(4) of Regulation
S-K.


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ITEM 3. QUANTITATIVE AND QUALITATIVE
DISCLOSURES ABOUT MARKET RISK .




Not
applicable.




ITEM
4T. CONTROLS AND PROCEDURES.




We
maintain disclosure controls and procedures that are designed to ensure that
information required to be disclosed in the reports that we file with, or submit
to, the Securities and Exchange Commission (the "SEC") under the Securities
Exchange Act of 1934 (the "Exchange Act") is recorded, processed, summarized and
reported within the time periods specified in the SEC's rules and forms and that
such information is accumulated and communicated to our management, including
our chief executive and financial officers, as appropriate, to allow timely
decisions regarding required disclosure. As required by SEC Rule 13a-15(b), we
carried out an evaluation, under the supervision and with the participation of
our management, including our chief executive and financial officers, of the
effectiveness of the design and operation of' our disclosure controls and
procedures as of the end of the period covered by this report.  Based
on that evaluation, our chief executive and financial officers concluded that
our disclosure controls and procedures were effective as of the end of the
period covered by this report.





Based
upon our evaluation, we also concluded that there was no change in our internal
control over financial reporting during our most recent fiscal quarter that has
materially affected, or is reasonably likely to materially affect, our internal
control over financial reporting.




PART
II




ITEM 1.   LEGAL PROCEEDINGS
..




There
have been no material developments with respect to any of the legal proceedings
described in our previously filed Annual Report on Form 10-K.





ITEM
1A.  RISK FACTORS.





Information regarding risk factors
appears under “Risk Factors” included in Item 1, and “Item 6, Management’s
Discussion and Analysis of Financial Condition and Results of Operations” of our
Annual Report on Form 10-K for the year ended December 31, 2008 as filed with
the Securities and Exchange Commission.  Except as set forth below,
there have been no material changes from the risk factors previously disclosed
in that Annual Report on Form 10-K.





We
will need to obtain additional funding in the near future or we may have to
cease our operations.





As of the
date of the filing of this report, we do not have sufficient cash available to
adequately fund our current corporate operations.   We are
currently seeking additional funding from various sources, seeking certain fee
income transactions, and are considering certain strategic transactions and
sales agreements that may provide us with the funds necessary to continue to
operate and develop our Jatropha farms.  However, we do not have any
agreements in place for either additional funding or for any strategic
transactions, and no assurance can be given that we will be able to obtain
additional financing or enter into a strategic transaction.  If we do
not raise additional funds in the immediate future or otherwise protect our
business and assets in a strategic transaction, we will have to consider winding
down or fully stopping all of our operations, filing for bankruptcy, or
otherwise liquidating our company.  In either case, our shareholders
will lose their investment in our securities.





We
currently have outstanding a $475,000 short-term promissory notes that is
secured by a lien on all of this company’s assets.  Accordingly, a
default under the secured promissory note could result in the foreclosure of all
of our assets and the termination of our business.




We
currently have outstanding a $475,000 promissory note that is secured by a first
priority security interest on all of our assets.  The promissory note
is scheduled to mature on July 13, 2009.   Failure to fully repay
the outstanding principal balance, plus all interest that accrues on that
promissory note, upon maturity could result in the acceleration of the
promissory note and the foreclosure of our assets.  If we are unable
to repay the note in full upon its maturity, or if we otherwise default under
our obligations to the holders of the promissory note, the holders of the
promissory note will have the right to foreclose on all of our assets, which
would materially and adversely affect our ability to continue our operations and
could terminate our existence.  We currently do not have sufficient
funds to repay the loan, and no assurance can be given that we will be able to
repay the promissory note as scheduled.


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We may lose our newly acquired 400
acre Jatropha farm in Belize if we are unable to repay an outstanding U.S.
$303,611loan that is secured by a mortgage
on the farm.





We have
entered into an agreement to acquire all of the outstanding capital stock of
Technology Alternatives Limited, a company that owns and operates a 400 acre
Jatropha farm in Belize.  As part of the purchase price, we have
agreed to issue four loans, having an aggregate balance of U.S. $303,611 and a
maturity date of six months following the closing of the
transaction.  These loans will be secured by a first lien on the
Belizean Jatropha farm.  We currently do not have sufficient funds to
repay these loans by their anticipated maturity date.  Accordingly,
unless we obtain additional funds from the sale of our securities, from the sale
of some of our products, and/or from strategic transactions, we may lose our new
Belizean farm when the four loans mature, which loss will have a material
negative affect on our plans to develop our Central American Jatropha
operations.  No assurance can be given that we will be able to raise
the funds needed to repay the $303,611 loans.




ITEM 2.   UNREGISTERED SALES OF EQUITY
SECURITIES AND USE OF PROCEEDS .




None




ITEM 3.   DEFAULTS UPON SENIOR
SECURITIES .




None.




ITEM 4.   SUBMISSION OF MATTERS TO A VOTE OF
SECURITY HOLDERS .




None.




ITEM 5.   OTHER INFORMATION




None.





ITEM 6.   EXHIBITS




10.1
            
            Stock
      Purchase Agreement, dated March __, 2009, between the Global Clean Energy
      Holdings, Inc. and the four shareholders of Technology Alternatives
      Limited, a Belizean Company formed under the Laws of Belize.  This
      agreement replaces the Stock Purchase Agreement, dated October 30,
      2008.31.1
            
            Rule
      13a-14(a) Certification, as adopted pursuant to Section 302 of the
      Sarbanes-Oxley Act of 200231.2
            
            Rule
      13a-14(a) Certification, as adopted pursuant to Section 302 of the
      Sarbanes-Oxley Act of 200232.1
            
            Certification
      pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of
      the Sarbanes-Oxley Act of 200232.2
            
            Certification
      pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of
      the Sarbanes-Oxley Act of 2002


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SIGNATURES




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




GLOBAL
      CLEAN ENERGY HOLDINGS, INC.Date:
      May 20, 2009
                  By:
                  /s/
      Bruce K. NelsonBruce
      K. Nelson
                    Chief
      Financial
Officer


24