Biofuel policies under the Renewable Fuel Standard (RFS) housed in the CAA and administered by EPA and under the Internal Revenue Code administered by the Internal Revenue Service are reviewed to demonstrate inconsistencies not only between the statutes, but also the regulations developed by each agency. The lack of harmonization creates unintended consequences of some fuels reaping government incentives and others, being used in similar applications and delivering equitable environmental benefits, receiving no government assistance in the form of tax credits or participating in the RFS. Environmental, end-use applications, fuel property requirements, and financial incentive differences are discussed.