Several studies have linked diesel engine exhaust particulate matter (DPM) to adverse health effects. To examine the effects of biodiesel blends on light-duty diesel engine exhaust composition, concentrations of a select number of target compounds were determined in petrodiesel-biodiesel [waste vegetable oil (WVO) and soybean (SOY) feedstocks] fuel blends, lubricating oil, and exhaust particulate matter (PM). Particulate matter was generated from a light-duty diesel engine running on a transient drive cycle and fueled with WVO (B10, B20, B50, and B100 where Bxx refers to volume % biodiesel in fuel blend) and SOY (B20 and B100) biodiesel fuels blended with ultralow sulfur diesel (ULSD) reference fuel (B00). As expected, concentrations of individual n-alkanes (C-12-C-24) decreased with increasing biodiesel content but were absent from B100 for both WVO and SOY feedstocks. No target PAHs, carbonyls, and quinones were detected in B00 fuel, biodiesel fuel blends (for both WVO and SOY), or lubricating oil. No FAMEs were detected in the neat petrodiesel fuel or lubricating oil, but, for exhaust PM, total FAMEs emissions increased, percent composition varied, and the PM cis/trans FAMEs isomer ratio decreased with increasing biodiesel for both feedstocks. Particle phase emission rates of the total aliphatic aldehydes in WVO blends increased by 0.02-2.49 ng/mu g(PM) (56-4804%), and in SOY B20 and B100 blends were 0.05 and 0.49 ng/mu g(PM) (106% and 1203%) higher than the petrodiesel emissions, respectively. In contrast, emission rates of target aromatics (aldehydes, ketones) and quinones in both the WVO and SOY blends generally decreased with increasing biodiesel in the fuel. Overall, the absence of aromatic compounds in biodiesel fuels led to 3-50% lower quinone emissions in biodiesel exhaust PM for the B10 to B50 blends and complete removal of quinones in the exhaust when operating on 100% neat biodiesel. FAMEs identified as the precursors to aliphatic aldehydes were polyunsaturated methyl linoleate and possibly methyl linolenate. Monounsaturated methyl oleate and saturated methyl palmitate proportions relatively increased in PM compared to fuel. Both fuel endmembers contributed fuel components to exhaust but at different mass fractions. n-Alkanes in exhaust PM, originating from petrodiesel fuel, represented 0.1-0.9 of the injected fuel mass, and FAMEs from biodiesel were a much smaller exhaust mass fraction (similar to 10(-5)). Use of WVO and SOY biodiesel blends in a light-duty diesel engine resulted in significant emission reductions of some toxic and mutagenic compounds (aromatic carbonyls and quinones) but an increase in emission of other toxic compounds (low molecular weight aliphatic carbonyls with less than 10 carbon atoms) previously reported to induce oxidative stress in cells. Future work needs to quantify relationships between fuel composition/properties, gas vs particle toxic polar combustion products, and their potential to induce variable biological effects that lead to adverse outcomes.