There has been criticism that corn ethanol is not as clean a fuel source as claimed. The industry has been lobbying to have investigators exclude emissions from land use changes when evaluating GHG released from the biofuel and to only count tail pipe emissions. However, the EPA found indirect emissions, mostly from land clearing, are a major source of heat-trapping pollution in the corn ethanol industry.

Corn ethanol is increasing worldwide demand on food crops, promoting clearing of previously untouched land to grow new crops. These forests are a major carbon sink and clearing them to make a "green" fuel is counter productive.

Experts are now advising that to meet the 2005 EPA Renewable Fuel Standards, fuels from grass, wood chips and other waste material are better options, but these other biofuels need technology that is not as advanced.