The primary objective of this study was to evaluate the impact of three different biodiesel feedstocks on emissions compared to a baseline CARB ULSD with two heavy-duty trucks equipped with and without aftertreatment technologies. The biodiesels included a soybean oil methyl ester (SME), a waste cooking oil methyl ester (WCO), and a methyl ester obtained from animal fat (AFME), blended at a 50% level by volume with the CARB diesel. The vehicles were equipped with a 2010 Cummins ISX-15 engine with a selective catalytic reduction (SCR), diesel oxidation catalyst (DOC) and a diesel particulate filter (DPF) and with a 2002 Cummins ISX-450 engine. Both vehicles were tested over the Urban Dynamometer Driving Schedule (UDDS) on a heavy-duty chassis dynamometer. For this study, nitrogen oxides (NOx), carbon monoxide (CO), carbon dioxide (CO2), total hydrocarbons (THC), methane (CH4), non-methane hydrocarbons (NMHC), and particulate matter (PM) were measured. In conjunction with these measurements, unregulated emissions, including ammonia (NH3), carbonyl compounds, and light aromatic hydrocarbons were measured for both vehicles. Ultrafine particles were also investigated with total particle number and particle size distributions. The redox activity, measured by the dithiothreitol (DTT) assay, was determined for both the vapor and particle-phase components of PM.The results showed that biodiesel reduced PM, THC, and CO emissions for the older vehicle, while increasing NOx emissions, consistent with the trends typically seen for biodiesel fuels on engines without any aftertreatment. For the 2010 vehicle, higher NOx and lower CO emissions were still seen for the biodiesel fuels, even at the lower emission levels for this vehicle. THC and PM emissions, on the other hand, were reduced to very low levels for the 2010 vehicle, and did not show any fuel trends. CO2 emissions were similar for the different fuels for both vehicles. Particle size distributions for the older engine showed bimodal particle distributions with both nucleation and accumulation mode particles, while the newer vehicle showed a strong nucleation mode for all fuels. Formaldehyde and acetaldehyde were the dominant carbonyls in the exhaust for both vehicles, with biodiesel showing some reductions in their emissions relative to CARB ULSD. For the redox activity, the biodiesel fuels had less prooxidant activity than the ULSD.