The impacts of biodiesel and a continuously regenerated (catalyzed) diesel particle filter (DPF) on the emissions of volatile unburned hydrocarbons, carbonyls, and particle associated polycyclic aromatic hydrocarbons (PAH) and nitro-PAH, were investigated. Experiments were conducted on a 5.9 L Cummins ISB, heavy-duty diesel engine using certification ultra-low-sulfur diesel (ULSD, S ≤ 15 ppm), soy biodiesel (B100), and a 20% blend thereof (B20). Against the ULSD baseline, B20 and B100 reduced engine-out emissions of measured unburned volatile hydrocarbons and PM associated PAH and nitro-PAH by significant percentages (40% or more for B20 and higher percentage for B100). However, emissions of benzene were unaffected by the presence of biodiesel and emissions of naphthalene actually increased for B100. This suggests that the unsaturated FAME in soy-biodiesel can react to form aromatic rings in the diesel combustion environment. Methyl acrylate and methyl 3-butanoate were observed as significant species in the exhaust for B20 and B100 and may serve as markers of the presence of biodiesel in the fuel. The DPF was highly effective at converting gaseous hydrocarbons and PM associated PAH and total nitro-PAH. However, conversion of 1-nitropyrene by the DPF was less than 50% for all fuels. Blending of biodiesel caused a slight reduction in engine-out emissions of acrolein, but otherwise had little effect on carbonyl emissions. The DPF was highly effective for conversion of carbonyls, with the exception of formaldehyde. Formaldehyde emissions were increased by the DPF for ULSD and B20.