The use of biodiesel fuels derived from vegetable oils or animal fats as a substitute for conventional petroleum fuel in diesel engines has received increased attention. This interest is based on a number of properties of biodiesel including the fact that it is produced from a renewable resource, its biodegradability, and its potential beneficial effects on exhaust emissions. As part of Tier 1 compliance requirements for EPA's Fuel Registration Program, a detailed chemical characterization of the transient exhaust emissions from three modern diesel engines was performed, both with and without an oxidation catalyst. This characterization included several forms of hydrocarbon speciation, as well as measurement of aldehydes, ketones, and alcohols. In addition, both particle-phase and semivolatile-phase PAH and nitro-PAH compounds were measured. Unregulated emissions were characterized with neat biodiesel and with a blend of biodiesel and conventional diesel fuel. Chemical characterization revealed lower levels of some toxic and reactive hydrocarbon species when biodiesel fuels were used. In addition, emissions of PAH and nitro PAH compounds were substantially lower with biodiesel, as compared to conventional diesel fuel.