Biofuels, such as bio-ethanol, bio-butanol, and biodiesel, are of increasing interest as alternatives to petroleum-based transportation fuels because they offer the long-term promise of fuel-source regenerability and reduced climatic impact. Current discussions emphasize the processes to make such alternative fuels and fuel additives, the compatibility of these substances with current fuel-delivery infrastructure and engine performance, and the competition between biofuel and food production. However, the combustion chemistry of the compounds that constitute typical biofuels, including alcohols, ethers, and esters, has not received similar public attention. Herein we highlight some characteristic aspects of the chemical pathways in the combustion of prototypical representatives of potential biofuels. The discussion focuses on the decomposition and oxidation mechanisms and the formation of undesired, harmful, or toxic emissions, with an emphasis on transportation fuels. New insights into the vastly diverse and complex chemical reaction networks of biofuel combustion are enabled by recent experimental investigations and complementary combustion modeling. Understanding key elements of this chemistry is an important step towards the intelligent selection of next-generation alternative fuels.