Filed
      Pursuant to Rule 424(b)(3)
    Registration
      File No. 333-127714
     
    PACIFIC
      ETHANOL, INC.
    
    PROSPECTUS
      SUPPLEMENT NO. 2 DATED JUNE 23, 2006
    TO
      FINAL PROSPECTUS DATED APRIL 24, 2006
     
    The
      final
      prospectus of Pacific Ethanol, Inc. dated April 24, 2006 is supplemented to
      include the following updated information:
     
    Risk
      Factors
     
    The
      Risk
      Factors section is amended and restated in its entirety to read as
      follows:
     
    RISK
      FACTORS
     
    The
      following summarizes material risks that you should carefully consider before
      you decide to buy our common stock in this offering. Any of the following risks,
      if they actually occur, would likely harm our business, financial condition
      and
      results of operations. As a result, the trading price of our common stock could
      decline, and you could lose the money you paid to buy our common
      stock.
     
    Risks
      Related to our Combined Operations
     
    We
      have incurred significant losses in the past and we may incur significant losses
      in the future. If we continue to incur losses, we will experience negative
      cash
      flow, which may hamper our operations, may prevent us from expanding our
      business and may cause our stock price to decline. 
     
    We
      have
      incurred losses in the past. As of March 31, 2006, we had an accumulated deficit
      of approximately $14.2 million. For the three months ended March 31, 2006,
      we
      incurred a net loss of approximately $600,000. For the year ended
      December 31, 2005, we incurred a net loss of approximately $9.9 million. We
      expect to incur losses for the foreseeable future and at least until the
      completion of our first ethanol production facility in Madera County. We
      estimate that the earliest completion date of this facility and, as a result,
      our earliest date of ethanol production, will not occur until the fourth quarter
      of 2006. We expect to rely on cash on hand, cash, if any, generated from our
      operations and financings to fund all of the cash requirements of our business.
      If our net losses continue, we will experience negative cash flow, which may
      hamper current operations and may prevent us from expanding our business. We
      may
      be unable to attain, sustain or increase profitability on a quarterly or annual
      basis in the future. If we do not achieve, sustain or increase profitability
      our
      stock price may decline.
     
    The
      high concentration of our sales within the ethanol production and marketing
      industry could result in a significant reduction in sales and negatively affect
      our profitability if demand for ethanol declines. 
     
    Our
      revenue is and will continue to be derived primarily from sales of ethanol.
      Currently, the predominant oxygenate used to blend with gasoline is ethanol.
      Ethanol competes with several other existing products and other alternative
      products could also be developed for use as fuel additives. We expect to be
      completely focused on the production and marketing of ethanol and its
      co-products for the foreseeable future. We may be unable to shift our business
      focus away from the production and marketing of ethanol to other renewable
      fuels
      or competing products. Accordingly, an industry shift away from ethanol or
      the
      emergence of new competing products may reduce the demand for ethanol. A
      downturn in the demand for ethanol would significantly and adversely affect
      our
      sales and profitability.
    
     
    If
      the expected increase in ethanol demand does not occur, or if the demand for
      ethanol decreases, there may be excess capacity in our industry.
     
    Domestic
      ethanol production capacity has increased steadily from 1.7 billion gallons
      per
      year in January of 1999 to 4.8 billion gallons per year at June 2006 according
      to the Renewable Fuels Association, or RFA. In addition, there is a significant
      amount of capacity being added to our industry. We believe that approximately
      2.0 billion gallons per year of production capacity is currently under
      construction. This capacity is being added to address anticipated increases
      in
      demand. Moreover, under the United States Department of Agriculture’s CCC
      Bioenergy Program, which is scheduled to expire September 30, 2006, the federal
      government makes payments of up to $150.0 million annually to ethanol producers
      that increase their production. This could create an additional incentive to
      develop excess capacity. However, demand for ethanol may not increase as quickly
      as expected, or at all. If the ethanol industry has excess capacity, a fall
      in
      prices will likely occur which will have an adverse impact on our results of
      operations, cash flows and financial condition. Excess capacity may result
      from
      the increases in capacity coupled with insufficient demand. Demand could be
      impaired due to a number of factors, including regulatory developments and
      reduced United States gasoline consumption. Reduced gasoline consumption could
      occur as a result of increased gasoline or oil prices. For example, price
      increases could cause businesses and consumers to reduce driving or acquire
      vehicles with more favorable gasoline mileage capabilities.
     
    We
      rely heavily on our President and Chief Executive Officer, Neil Koehler. The
      loss of his services could adversely affect our ability to source ethanol from
      our key suppliers and our ability to sell ethanol to our customers.
     
    Our
      success depends, to a significant extent, upon the continued services of Neil
      Koehler, who is our President and Chief Executive Officer. For example, Mr.
      Koehler has developed key personal relationships with our ethanol suppliers
      and
      customers. We greatly rely on these relationships in the conduct of our
      operations and the execution of our business strategies. The loss of Mr. Koehler
      could, therefore, result in the loss of our favorable relationships with one
      or
      more of our ethanol suppliers and customers. In addition, Mr. Koehler has
      considerable experience in the construction, start-up and operation of ethanol
      production facilities and in the ethanol marketing business. Although we have
      entered into an employment agreement with Mr. Koehler, that agreement is of
      limited duration and is subject to early termination by Mr. Koehler under
      certain circumstances. In addition, we do not maintain “key person” life
      insurance covering Mr. Koehler or any other executive officer. The loss of
      Mr.
      Koehler could also significantly delay or prevent the achievement of our
      business objectives.
     
    Our
      independent registered public accounting firm has advised management and our
      audit committee that they have identified a material weakness in our internal
      controls and we have concluded that we have a material weakness in our
      disclosure controls and procedures. Our business and stock price may be
      adversely affected if we do not remediate this material weakness or if we have
      other material weaknesses in our internal controls.
     
    In
      connection with its audit of our consolidated financial statements for the
      year
      ended December 31, 2005, our independent registered public accounting firm
      advised management of the following matter that the accounting firm considered
      to be a material weakness: The current organization of our accounting department
      does not provide us with the appropriate resources and adequate technical skills
      to accurately account for and disclose our activities. Our resources to produce
      reliable financial reports and fulfill our other obligations as a public company
      are limited due to our small number of employees and the limited public company
      experience of our management. The existence of one or more material weaknesses
      in our internal controls could result in errors in our financial statements
      and
      substantial costs and resources may be required to rectify these material
      weaknesses. If we are unable to produce reliable financial reports, investors
      could lose confidence in our reported financial information, the market price
      of
      our stock could decline significantly, we may be unable to obtain additional
      financing to operate and expand our business, and our business and financial
      condition could be harmed. 
    
     
    The
      United States ethanol industry is highly dependent upon a myriad of federal
      and
      state legislation and regulation and any changes in such legislation or
      regulation could materially adversely affect our results of operations and
      financial condition.
     
    The
      elimination or significant reduction in the Federal Excise Tax Credit could
      have
      a material adverse effect on our results of operations.
     
    The
      production of ethanol is made significantly more competitive by federal tax
      incentives. The Federal Excise Tax Credit, or FETC, program, which is scheduled
      to expire on December 31, 2010, allows gasoline distributors who blend ethanol
      with gasoline to receive a federal excise tax rate reduction for each blended
      gallon they sell regardless of the blend rate. The current federal excise tax
      on
      gasoline is $0.184 per gallon, and is paid at the terminal by refiners and
      marketers. If the fuel is blended with ethanol, the blender may claim a $0.51
      tax credit for each gallon of ethanol used in the mixture. The FETC may not
      be
      renewed prior to its expiration in 2010, or if renewed, it may be renewed on
      terms significantly less favorable than current tax incentives. The elimination
      or significant reduction in the FETC could have a material adverse effect on
      our
      results of operations.
     
    Waivers
      of the Renewable Fuels Standard minimum levels of renewable fuels included
      in
      gasoline could have a material adverse affect on our results of
      operations.
     
    Under
      the
      Energy Policy Act of 2005, the Department of Energy, in consultation with the
      Secretary of Agriculture and the Secretary of Energy, may waive the Renewable
      Fuels Standard, or RFS, mandate with respect to one or more states if the
      Administrator determines that implementing the requirements would severely
      harm
      the economy or the environment of a state, a region or the United States, or
      that there is inadequate supply to meet the requirement. In addition, the
      Department of Energy was directed under the Energy Policy Act of 2005 to conduct
      a study by January 2006 to determine if the RFS will have a severe adverse
      impact on consumers in 2006 on a national, regional or state basis. Based on
      the
      results of the study, the Secretary of Energy must make a recommendation to
      the
      EPA as to whether the RFS should be waived for 2006. Any waiver of the RFS
      with
      respect to one or more states or with respect to 2006 would adversely offset
      demand for ethanol and could have a material adverse effect on our results
      of
      operations and financial condition.
     
    While
      the Energy Policy Act of 2005 imposes the RFS, it does not mandate the use
      of
      ethanol and eliminates the oxygenate requirement for reformulated gasoline
      in
      the Reformulated Gasoline Program included in the Clean Air
      Act.
     
    The
      Reformulated Gasoline, or RFG, program’s oxygenate requirements contained in the
      Clean Air Act, which, according to the RFA, accounted for approximately 2.0
      billion gallons of ethanol use in 2004, was completely eliminated on May 5,
      2006
      by the Energy Policy Act of 2005. While the RFA expects that ethanol should
      account for the largest share of renewable fuels produced and consumed under
      the
      RFS, the RFS is not limited to ethanol and also includes biodiesel and any
      other
      liquid fuel produced from biomass or biogas. The elimination of the oxygenate
      requirement for reformulated gasoline in the RFG program included in the Clean
      Air Act may result in a decline in ethanol consumption in favor of other
      alternative fuels, which in turn could have a material adverse effect on our
      results of operations and financial condition. 
    
     
    We
      may be adversely affected by environmental, health and safety laws, regulations
      and liabilities.
     
    We
      are
      subject to various federal, state and local environmental laws and regulations,
      including those relating to the discharge of materials into the air, water
      and
      ground, the generation, storage, handling, use, transportation and disposal
      of
      hazardous materials, and the health and safety of our employees. In addition,
      some of these laws and regulations require our facilities to operate under
      permits that are subject to renewal or modification. These laws, regulations
      and
      permits can often require expensive pollution control equipment or operational
      changes to limit actual or potential impacts to the environment. A violation
      of
      these laws and regulations or permit conditions can result in substantial fines,
      natural resource damages, criminal sanctions, permit revocations and/or facility
      shutdowns. In addition, we have made, and expect to make, significant capital
      expenditures on an ongoing basis to comply with increasingly stringent
      environmental laws, regulations and permits. 
     
    We
      may be
      liable for the investigation and cleanup of environmental contamination at
      each
      of the properties that we own or operate and at off-site locations where we
      arrange for the disposal of hazardous substances. If these substances have
      been
      or are disposed of or released at sites that undergo investigation and/or
      remediation by regulatory agencies, we may be responsible under the
      Comprehensive Environmental Response, Compensation and Liability Act of 1980,
      or
      CERCLA, or other environmental laws for all or part of the costs of
      investigation and/or remediation, and for damages to natural resources. We
      may
      also be subject to related claims by private parties alleging property damage
      and personal injury due to exposure to hazardous or other materials at or from
      those properties. Some of these matters may require us to expend significant
      amounts for investigation, cleanup or other costs. 
     
    In
      addition, new laws, new interpretations of existing laws, increased governmental
      enforcement of environmental laws or other developments could require us to
      make
      additional significant expenditures. Continued government and public emphasis
      on
      environmental issues can be expected to result in increased future investments
      for environmental controls at our production facilities. Present and future
      environmental laws and regulations (and interpretations thereof) applicable
      to
      our operations, more vigorous enforcement policies and discovery of currently
      unknown conditions may require substantial expenditures that could have a
      material adverse effect on our results of operations and financial position.
      
     
    The
      hazards and risks associated with producing and transporting our products (such
      as fires, natural disasters, explosions, and abnormal pressures and blowouts)
      may also result in personal injury claims or damage to property and third
      parties. As protection against operating hazards, we maintain insurance coverage
      against some, but not all, potential losses. However, we could sustain losses
      for uninsurable or uninsured risks, or in amounts in excess of existing
      insurance coverage. Events that result in significant personal injury or damage
      to our property or third parties or other losses that are not fully covered
      by
      insurance could have a material adverse effect on our results of operations
      and
      financial position. 
     
    Our
      failure to manage our growth effectively could prevent us from achieving our
      goals.
     
    Our
      strategy envisions a period of rapid growth that may impose a significant burden
      on our administrative and operational resources. The growth of our business,
      and
      in particular, the completion of construction of our planned ethanol production
      facilities, will require significant investments of capital and management’s
      close attention. We have also entered into significant marketing agreements
      with
      Front Range Energy, LLC and Phoenix Bio-Industries, LLC, and we are seeking
      to
      enter into additional similar agreements with companies that currently, or
      expect to, produce ethanol, all of which may result in a substantial growth
      in
      our marketing business. Our ability to effectively manage our growth will
      require us to substantially expand the capabilities of our administrative and
      operational resources and to attract, train, manage and retain qualified
      management, technicians and other personnel. We may be unable to do so. In
      addition, our failure to successfully manage our growth could result in our
      sales not increasing commensurately with our capital investments. If we are
      unable to successfully manage our growth, we may be unable to achieve our
      goals.
    
     
    The
      ethanol production and marketing industry is extremely competitive. Many of
      our
      significant competitors have greater financial and other resources than we
      do
      and one or more of these competitors could use their greater resources to gain
      market share at our expense. In addition, certain of our suppliers may
      circumvent our marketing services, causing our sales and profitability to
      decline.
     
    The
      ethanol production and marketing industry is extremely competitive. Many of
      our
      significant competitors in the ethanol production and marketing industry, such
      as Archer Daniels Midland Company, or ADM, Cargill, Inc., VeraSun Energy
      Corporation, Aventine Renewable Energy, Inc., and Abengoa Bioenergy Corp.,
      have
      substantially greater production, financial, research and development, personnel
      and marketing resources than we do. In addition, we are not currently producing
      any ethanol that we sell and therefore are unable to capture the higher gross
      profit margins generally associated with production activities. As a result,
      our
      competitors, who are presently producing ethanol, may have greater relative
      advantages resulting from greater capital resources due to higher gross profit
      margins. As a result, our competitors may be able to compete more aggressively
      and sustain that competition over a longer period of time than we could. Our
      lack of resources relative to many of our significant competitors may cause
      us
      to fail to anticipate or respond adequately to new developments and other
      competitive pressures. This failure could reduce our competitiveness and cause
      a
      decline in our market share, sales and profitability.
     
    In
      addition, some of our suppliers are potential competitors and, especially if
      the
      price of ethanol remains at historically high levels, they may seek to capture
      additional profits by circumventing our marketing services in favor of selling
      directly to our customers. If one or more of our major suppliers, or numerous
      smaller suppliers, circumvent our marketing services, our sales and
      profitability will decline.
     
    We
      also
      face increasing competition from international suppliers. Although there is
      a
      $0.54 per gallon tariff, which is scheduled to expire in 2007, on
      foreign-produced ethanol that is approximately equal to the blenders’ credit,
      ethanol imports equivalent to up to 7% of total domestic production in any
      given
      year from various countries were exempted from this tariff under the Caribbean
      Basin Initiative to spur economic development in Central America and the
      Caribbean. Currently, international suppliers produce ethanol primarily from
      sugar cane and have cost structures that are generally substantially lower
      than
      ours. 
     
    Any
      increase in domestic or foreign competition could cause us to reduce our prices
      and take other steps to compete effectively, which could adversely affect our
      results of operations and financial position. 
     
    We
      may engage in hedging transactions and other risk mitigation strategies that
      could harm our results.
     
    In
      an
      attempt to partially offset the effects of volatility of ethanol prices and
      corn
      and natural gas costs, we may enter into contracts to supply a portion of our
      ethanol production or purchase a portion of our corn or natural gas requirements
      on a forward basis and may also engage in other hedging transactions involving
      exchange-traded futures contracts for corn, natural gas and unleaded gasoline
      from time to time. The financial statement impact of these activities is
      dependent upon, among other things, the prices involved and our ability to
      sell
      sufficient products to use all of the corn and natural gas for which we have
      futures contracts. Hedging arrangements also expose us to the risk of financial
      loss in situations where the other party to the hedging contract defaults on
      its
      contract or, in the case of exchange-traded contracts, where there is a change
      in the expected differential between the underlying price in the hedging
      agreement and the actual prices paid or received by us. Hedging activities
      can
      themselves result in losses when a position is purchased in a declining market
      or a position is sold in a rising market. A hedge position is often settled
      in
      the same time frame as the physical commodity is either purchased, as in the
      case of corn and natural gas, or sold as in the case of ethanol. Hedging losses
      may be offset by a decreased cash price for corn and natural gas and an
      increased cash price for ethanol. We also vary the amount of hedging or other
      risk mitigation strategies we undertake, and we may choose not to engage in
      hedging transactions at all. As a result, our results of operations and
      financial position may be adversely affected by increases in the price of corn
      or natural gas or decreases in the price of ethanol or unleaded
      gasoline.
     
    
     
    Risks
      Relating to the Business of Kinergy
     
    Kinergy’s
      purchase and sale commitments as well as its inventory of ethanol held for
      sale
      subject us to the risk of fluctuations in the price of ethanol, which may result
      in lower or even negative gross profit margins and which could materially and
      adversely affect our profitability.
     
    Kinergy’s
      purchases and sales of ethanol are not always matched with sales and purchases
      of ethanol at prevailing market prices. Kinergy commits from time to time to
      the
      sale of ethanol to its customers without corresponding and commensurate
      commitments for the supply of ethanol from its suppliers, which subjects us
      to
      the risk of an increase in the price of ethanol. Kinergy also commits from
      time
      to time to the purchase of ethanol from its suppliers without corresponding
      and
      commensurate commitments for the purchase of ethanol by its customers, which
      subjects us to the risk of a decline in the price of ethanol. In addition,
      Kinergy increases inventory levels in anticipation of rising ethanol prices
      and
      decreases inventory levels in anticipation of declining ethanol prices. As
      a
      result, Kinergy is subject to the risk of ethanol prices moving in unanticipated
      directions, which could result in declining or even negative gross profit
      margins. Accordingly, our business is subject to fluctuations in the price
      of
      ethanol and these fluctuations may result in lower or even negative gross
      margins and which could materially and adversely affect our
      profitability.
     
    Kinergy
      depends on a small number of customers for the vast majority of its sales.
      A
      reduction in business from any of these customers could cause a significant
      decline in our overall sales and profitability.
     
    The
      vast
      majority of Kinergy’s sales are generated from a small number of customers.
      During 2005, sales to Kinergy’s three largest customers, each of whom accounted
      for 10% or more of total net sales, represented approximately 18%, 11% and
      10%,
      respectively, representing an aggregate of approximately 39%, of Kinergy’s total
      net sales. During 2004, sales to Kinergy’s four largest customers, each of whom
      accounted for 10% or more of total net sales, represented approximately 13%,
      12%, 12% and 12%, respectively, representing an aggregate of approximately
      49%,
      of Kinergy’s total net sales. We expect that Kinergy will continue to depend for
      the foreseeable future upon a small number of customers for a significant
      portion of its sales. Kinergy’s agreements with these customers generally do not
      require them to purchase any specified amount of ethanol or dollar amount of
      sales or to make any purchases whatsoever. Therefore, in any future period,
      Kinergy’s sales generated from these customers, individually or in the
      aggregate, may not equal or exceed historical levels. If sales to any of these
      customers cease or decline, Kinergy may be unable to replace these sales with
      sales to either existing or new customers in a timely manner, or at all. A
      cessation or reduction of sales to one or more of these customers could cause
      a
      significant decline in our overall sales and profitability.
     
    Kinergy’s
      lack of long-term ethanol orders and commitments by its customers could lead
      to
      a rapid decline in our sales and profitability.
     
    Kinergy
      cannot rely on long-term ethanol orders or commitments by its customers for
      protection from the negative financial effects of a decline in the demand for
      ethanol or a decline in the demand for Kinergy’s services. The limited certainty
      of ethanol orders can make it difficult for us to forecast our sales and
      allocate our resources in a manner consistent with our actual sales. Moreover,
      our expense levels are based in part on our expectations of future sales and,
      if
      our expectations regarding future sales are inaccurate, we may be unable to
      reduce costs in a timely manner to adjust for sales shortfalls. Furthermore,
      because Kinergy depends on a small number of customers for a significant portion
      of its sales, the magnitude of the ramifications of these risks is greater
      than
      if Kinergy’s sales were less concentrated within a small number of customers. As
      a result of Kinergy’s lack of long-term ethanol orders and commitments, we may
      experience a rapid decline in our sales and profitability.
    
     
    Kinergy
      depends on a small number of suppliers for the vast majority of the ethanol
      that
      it sells. If any of these suppliers is unable or decides not to continue to
      supply Kinergy with ethanol in adequate amounts, Kinergy may be unable to
      satisfy the demands of its customers and our sales, profitability
      and relationships with our customers will be adversely
      affected.
     
    Kinergy
      depends on a small number of suppliers for the vast majority of the ethanol
      that
      it sells. During 2005, Kinergy’s three largest suppliers, each of whom accounted
      for 10% or more of total purchases, represented approximately 22%, 20%, and
      17%,
      respectively, of purchases, representing an aggregate of approximately 59%,
      of
      the total ethanol Kinergy purchased for resale. During 2004, Kinergy’s three
      largest suppliers, each of whom accounted for 10% or more of the total
      purchases, represented approximately 27%, 23% and 14%, respectively, of
      purchases, representing an aggregate of approximately 64% of the total ethanol
      Kinergy purchased for resale. We expect that Kinergy will continue to depend
      for
      the foreseeable future upon a small number of suppliers for a significant
      majority of the ethanol that it purchases. In addition, Kinergy sources the
      ethanol that it sells primarily from suppliers in the Midwestern United States.
      The delivery of the ethanol that Kinergy sells is therefore subject to delays
      resulting from inclement weather and other conditions. Also, there is currently
      a substantial demand for ethanol which has, for most of 2005, far exceeded
      ethanol production capacities and Kinergy’s management has, from time to time,
      found it very difficult to satisfy all the demands for ethanol by Kinergy’s
      customers. If any of these suppliers is unable or declines for any reason to
      continue to supply Kinergy with ethanol in adequate amounts, Kinergy may be
      unable to replace that supplier and source other supplies of ethanol in a timely
      manner, or at all, to satisfy the demands of its customers. If this occurs,
      our
      sales and profitability and Kinergy’s relationships with its customers will be
      adversely affected.
     
    Risks
      Relating to the Business of PEI California
     
    We
      may not be able to implement our planned expansion
      strategy.
     
    We
      plan
      to grow our business by investing in new facilities and/or acquiring existing
      facilities and to pursue other business opportunities such as the production
      of
      other renewable fuels to the extent we deem those opportunities advisable.
      We
      believe that there is increasing competition for suitable sites. We may not
      find
      suitable additional sites for construction of new facilities, suitable
      acquisition candidates or other suitable expansion opportunities. 
     
    We
      may
      need additional financing to implement our expansion strategy and we may not
      have access to the funding required for the expansion of our business or such
      funding may not be available to us on acceptable terms. We may finance the
      expansion of our business with additional indebtedness or by issuing additional
      equity securities. We could face financial risks associated with incurring
      additional indebtedness, such as reducing our liquidity and access to financial
      markets and increasing the amount of cash flow required to service such
      indebtedness, or associated with issuing additional stock, such as dilution
      of
      ownership and earnings. 
     
    We
      must
      also obtain numerous regulatory approvals and permits in order to construct
      and
      operate additional or expanded facilities. These requirements may not be
      satisfied in a timely manner or at all. Federal and state governmental
      requirements may substantially increase our costs, which could have a material
      adverse effect on our results of operations and financial position. Our
      expansion plans may also result in other unanticipated adverse consequences,
      such as the diversion of management’s attention from our existing operations.
    
     
    Our
      construction costs may also increase to levels that would make a new facility
      too expensive to complete or unprofitable to operate. Except with respect to
      our
      Madera County facility, we have not entered into any construction contracts
      or
      other arrangements, other than site acquisition arrangements, that might limit
      our exposure to higher costs in developing and completing any new facilities.
      Contractors, engineering firms, construction firms and equipment suppliers
      also
      receive requests and orders from other ethanol companies and, therefore, we
      may
      not be able to secure their services or products on a timely basis or on
      acceptable financial terms. We may suffer significant delays or cost overruns
      as
      a result of a variety of factors, such as shortages of workers or materials,
      transportation constraints, adverse weather, unforeseen difficulties or labor
      issues, any of which could prevent us from commencing operations as expected
      at
      our facilities. 
     
    We
      may
      not find additional appropriate sites for new facilities and we may not be
      able
      to finance, construct, develop or operate these new facilities successfully.
      We
      also may be unable to find suitable acquisition candidates. Accordingly, we
      may
      not be able to implement our planned expansion strategy. 
     
    PEI
      California has not conducted any significant business operations and has been
      unprofitable to date.
      PEI California may be unsuccessful and decrease our overall profitability,
      causing us to fail to achieve one of our significant
      goals.
     
    PEI
      California has not conducted any significant business operations and has been
      unprofitable to date. Accordingly, there is no prior operating history by which
      to evaluate the likelihood of PEI California’s success or its contribution to
      our overall profitability. PEI California may not complete construction of
      all
      of our planned ethanol production facilities, and even if PEI California does
      complete the construction of all of our planned ethanol production facilities,
      PEI California may not be successful or contribute positively to our
      profitability. If PEI California is unsuccessful, it will decrease our overall
      profitability and we will have failed to achieve one of our significant goals.
      
     
    The
      raw materials and energy necessary to produce ethanol may be unavailable or
      may
      increase in price, adversely affecting our sales and profitability.
     
    The
      principal raw material we use to produce ethanol and ethanol by-products is
      corn. As a result, changes in the price of corn can significantly affect our
      business. In general, rising corn prices produce lower profit margins and,
      therefore, represent unfavorable market conditions. This is especially true
      since market conditions generally do not allow us to pass along increased corn
      costs to our customers because the price of ethanol is primarily determined
      by
      other factors, such as the price of oil and gasoline. At certain levels, corn
      prices may make ethanol uneconomical to use in markets where the use of fuel
      oxygenates is not mandated.
     
    The
      price
      of corn is influenced by general economic, market and regulatory factors. These
      factors include weather conditions, farmer planting decisions, government
      policies and subsidies with respect to agriculture and international trade
      and
      global demand and supply. The significance and relative impact of these factors
      on the price of corn is difficult to predict. Any event that tends to negatively
      impact the supply of corn will tend to increase prices and potentially harm
      our
      business. Corn bought by ethanol plants represented approximately 13% of the
      2005 total corn supply according to 2005 results reported by the National Corn
      Growers Association. The increasing ethanol capacity could boost demand for
      corn
      and result in increased prices for corn. 
     
    The
      production of ethanol also requires a significant amount of other raw materials
      and energy, primarily water, electricity and natural gas. For example, we
      estimate that our Madera County ethanol production facility will require
      significant and uninterrupted supplies of water, electricity and natural gas.
      The prices of electricity and natural gas have fluctuated significantly in
      the
      past and may fluctuate significantly in the future. Local water, electricity
      and
      gas utilities may not be able to reliably supply the water, electricity and
      natural gas that our facilities will need or may not be able to supply such
      resources on acceptable terms. In addition, if there is an interruption in
      the
      supply of water or energy for any reason, we may be required to halt ethanol
      production.
     
    
     
    The
      market price of ethanol is volatile and subject to significant fluctuations,
      which may cause our profitability
      to fluctuate significantly.
     
    The
      market price of ethanol is dependent upon many factors, including the price
      of
      gasoline, which is in turn dependent upon the price of petroleum. Petroleum
      prices are highly volatile and difficult to forecast due to frequent changes
      in
      global politics and the world economy. The distribution of petroleum throughout
      the world is affected by incidents in unstable political environments, such
      as
      Iraq, Iran, Kuwait, Saudi Arabia, the former U.S.S.R. and other countries and
      regions. The industrialized world depends critically upon oil from these areas,
      and any disruption or other reduction in oil supply can cause significant
      fluctuations in the prices of oil and gasoline. We cannot predict the future
      price of oil or gasoline and may establish unprofitable prices for the sale
      of
      ethanol due to significant fluctuations in market prices. For example, the
      price
      of ethanol declined by approximately 25% from its 2004 average price per gallon
      in five months from January 2005 through May 2005 and reversed this decline
      and
      increased to approximately 55% above its 2004 average price per gallon in four
      months from June 2005 through September 2005; and from September through
      December 2005, the price of ethanol trended downward, but reversed its trend
      in
      the first quarter of 2006 by rising approximately 16% above its 2005 average
      price per gallon. In recent years, the prices of gasoline, petroleum and ethanol
      have all reached historically unprecedented high levels. If the prices of
      gasoline and petroleum decline, we believe that the demand for and price of
      ethanol may be adversely affected. Fluctuations in the market price of ethanol
      may cause our profitability to fluctuate significantly.
     
    We
      believe that the production of ethanol is expanding rapidly. There are a number
      of new plants under construction and planned for construction, both inside
      and
      outside California. We expect existing ethanol plants to expand by increasing
      production capacity and actual production. Increases in the demand for ethanol
      may not be commensurate with increasing supplies of ethanol. Thus, increased
      production of ethanol may lead to lower ethanol prices. The increased production
      of ethanol could also have other adverse effects. For example, increased ethanol
      production could lead to increased supplies of co-products from the production
      of ethanol, such as wet distillers grain, or WDG. Those increased supplies
      could
      lead to lower prices for those co-products. Also, the increased production
      of
      ethanol could result in increased demand for corn. This could result in higher
      prices for corn and cause higher ethanol production costs and, in the event
      that
      PEI California is unable to pass increases in the price of corn to its
      customers, will result in lower profits. We cannot predict the future price
      of
      ethanol, WDG or corn. Any material decline in the price of ethanol or WDG,
      or
      any material increase in the price of corn, will adversely affect our sales
      and
      profitability.
     
    Certain
      countries can export ethanol to the United States duty-free, which may undermine
      the ethanol production industry in the United States.
     
    Imported
      ethanol is generally subject to a $0.54 per gallon tariff and a 2.5% ad valorem
      tax that was designed to offset the $0.51 per gallon ethanol subsidy available
      under the federal excise tax incentive program for refineries that blend ethanol
      in their fuel. There is a special exemption from the tariff for ethanol imported
      from 24 countries in Central America and the Caribbean islands which is limited
      to a total of 7.0% of United States production per year (with additional
      exemptions for ethanol produced from feedstock in the Caribbean region over
      the
      7.0% limit). In May 2006, bills were introduced in both the U.S. House of
      Representatives and U.S. Senate to repeal the $0.54 per gallon tariff. We do
      not
      know the extent to which the volume of imports would increase or the effect
      on
      United States prices for ethanol if this proposed legislation is enacted or
      if
      the tariff is not renewed beyond its current expiration in December 2007. In
      addition The North America Free Trade Agreement countries, Canada and Mexico,
      are exempt from duty. Imports from the exempted countries have increased in
      recent years and are expected to increase further as a result of new plants
      under development. In particular, the ethanol industry has expressed concern
      with respect to a new plant under development by Cargill, Inc., the fifth
      largest ethanol producer in the United States, in El Salvador that would take
      the water out of Brazilian ethanol and then ship the dehydrated ethanol from
      El
      Salvador to the United States duty-free. Since production costs for ethanol
      in
      Brazil are estimated to be significantly less than what they are in the United
      States, the import of the Brazilian ethanol duty-free through El Salvador or
      another country exempted from the tariff may negatively impact the demand for
      domestic ethanol and the price at which we sell our ethanol. 
    
     
    Risks
      Related to our Common Stock
     
    Our
      common stock has a small public float and shares of our common stock eligible
      for public sale could cause the market price of our stock to drop, even if
      our
      business is doing well, and make it difficult for us to raise additional capital
      through sales of equity securities.
     
    As
      of
      June 21, 2006, we had outstanding approximately 37.2 million shares of our
      common stock. Approximately 14.8 million of these shares were restricted
      under the Securities Act of 1933, including approximately 5.9 million shares
      beneficially owned, in the aggregate, by our executive officers, directors
      and
      10% stockholders. Accordingly, our common stock has a public float of
      approximately 22.4 million shares held by a relatively small number of
      public investors.
     
    We
      are in
      the process of registering for resale approximately 8.2 million shares of our
      common stock, including shares of our common stock underlying warrants. If
      and
      when the registration statement covering these shares of common stock is
      declared effective, holders of these shares will be permitted, subject to few
      limitations, to freely sell these shares of common stock. As a result of our
      small public float, sales of substantial amounts of common stock, including
      shares issued upon the exercise of stock options or warrants, or an anticipation
      that such sales could occur, may materially and adversely affect prevailing
      market prices for our common stock. Any adverse effect on the market price
      of
      our common stock could make it difficult for us to raise additional capital
      through sales of equity securities at a time and at a price that we deem
      appropriate.
     
    As
      a result of our issuance of shares of Series A Preferred Stock to Cascade
      Investment, L.L.C., our
      common stockholders may experience numerous negative effects and most of the
      rights of our common stockholders will be subordinate to the rights of Cascade
      Investment, L.L.C.
     
    As
      a
      result of our issuance of shares of Series A Preferred Stock to Cascade
      Investment, L.L.C., or Cascade, common stockholders may experience numerous
      negative effects, including substantial dilution. The 5,250,000 shares of Series
      A Preferred Stock issued to Cascade are immediately convertible into 10,500,000
      shares of our common stock, which amount, when issued, would, based upon the
      number of shares of our common stock outstanding as of June 21, 2006, represent
      approximately 22% of our shares outstanding and, in the event that we are
      profitable, would likewise result in a decrease in our earnings per share by
      approximately 22%, without taking into account cash or stock payable as
      dividends on the Series A Preferred Stock. In addition, income available to
      common stockholders will be reduced during the second quarter of 2006 to the
      extent that the market price of our common stock is in excess of the $8.00
      per
      share purchase price, on an as-converted basis, at which we issued the Series
      A
      Preferred Stock. This reduction will be calculated based on the number of shares
      of common stock deemed issued, on an as-converted basis, multiplied by the
      difference in the market price of our common stock and the $8.00 per share
      purchase price.
     
    Other
      negative effects to our common stockholders will include potential additional
      dilution from dividends paid in Series A Preferred Stock and certain
      antidilution adjustments. In addition, rights in favor of holders of our Series
      A Preferred Stock include: seniority in liquidation and dividend preferences;
      substantial voting rights; numerous protective provisions; the right to appoint
      two persons to our board of directors and periodically nominate two persons
      for
      election by our stockholders to our board of directors; preemptive rights;
      and
      redemption rights. Also, the Series A Preferred Stock could have the effect
      of
      delaying, deferring and discouraging another party from acquiring control of
      Pacific Ethanol. In addition, based on our current number of shares of common
      stock outstanding, Cascade has approximately 22% of all outstanding voting
      power
      as compared to approximately 12% of all outstanding voting power held in
      aggregate by our current executive officers and directors. Any of the above
      factors may materially and adversely affect our common stockholders and the
      values of their investments in our common stock. 
    
     
    Our
      stock price is highly volatile, which could result in substantial losses for
      investors purchasing shares of our common stock and in litigation against
      us.
     
    The
      market price of our common stock has fluctuated significantly in the past and
      may continue to fluctuate significantly in the future. The market price of
      our
      common stock may continue to fluctuate in response to one or more of the
      following factors, many of which are beyond our control:
    
    
      
          
            | 
               · 
             | 
            
               changing
                conditions in the ethanol and fuel markets; 
             | 
          
          
            | 
               · 
             | 
            
               the
                volume and timing of the receipt of orders for ethanol from major
                customers; 
             | 
          
          
            | 
               · 
             | 
            
               competitive
                pricing pressures; 
             | 
          
          
            | 
               · 
             | 
            
               our
                ability to produce, sell and deliver ethanol on a cost-effective
                and
                timely basis; 
             | 
          
          
            | 
               · 
             | 
            
               the
                introduction and announcement of one or more new alternatives to
                ethanol
                by our competitors; 
             | 
          
          
            | 
               · 
             | 
            
               changes
                in market valuations of similar companies; 
             | 
          
          
            | 
               · 
             | 
            
               stock
                market price and volume fluctuations generally; 
             | 
          
          
            | 
               · 
             | 
            
               regulatory
                developments or increased enforcement; 
             | 
          
          
            | 
               · 
             | 
            
               fluctuations
                in our quarterly or annual operating results; 
             | 
          
          
            | 
               · 
             | 
            
               additions
                or departures of key personnel; 
             | 
          
          
            | 
               · 
             | 
            
               our
                inability to obtain construction, acquisition, capital equipment
                and/or
                working capital financing; and 
             | 
          
          
            | 
               · 
             | 
            
               future
                sales of our common stock or other
                securities. 
             | 
          
      
     
     
    Furthermore,
      we believe that the economic conditions in California and other states, as
      well
      as the United States as a whole, could have a negative impact on our results
      of
      operations. Demand for ethanol could also be adversely affected by a slow-down
      in overall demand for oxygenate and gasoline additive products. The levels
      of
      our ethanol production and purchases for resale will be based upon forecasted
      demand. Accordingly, any inaccuracy in forecasting anticipated revenues and
      expenses could adversely affect our business. Furthermore, we recognize revenues
      from ethanol sales at the time of delivery. The failure to receive anticipated
      orders or to complete delivery in any quarterly period could adversely affect
      our results of operations for that period. Quarterly results are not necessarily
      indicative of future performance for any particular period, and we may not
      experience revenue growth or profitability on a quarterly or an annual
      basis.
     
    The
      price
      at which you purchase shares of our common stock may not be indicative of the
      price that will prevail in the trading market. You may be unable to sell your
      shares of common stock at or above your purchase price, which may result in
      substantial losses to you and which may include the complete loss of your
      investment. In the past, securities class action litigation has often been
      brought against a company following periods of stock price volatility. We may
      be
      the target of similar litigation in the future. Securities litigation could
      result in substantial costs and divert management’s attention and our resources
      away from our business. Any of the risks described above could adversely affect
      our sales and profitability and also the price of our common stock.
    
    (End
      of
      Prospectus Supplement No. 2.)
     
     
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