The emissions and the potential health effects of particulate matter (PM) were assessed from two heavy-duty trucks with and without emission control aftertreatment systems when operating on CARB ultra-low sulfur diesel (ULSD) and three different biodiesel blends. The CARB ULSD was blended with soy-based biodiesel, animal fat biodiesel, and waste cooking oil biodiesel at 50vol%. Testing was conducted over the EPA Urban Dynamometer Driving Schedule (UDDS) in triplicate for both trucks. The aftertreatment controls effectively decreased PM mass and number emissions, as well as the polycyclic aromatic hydrocarbons (PAHs) compared to the uncontrolled truck. Emissions of nitrogen oxides (NO) exhibited increases with the biodiesel blends, showing some feedstock dependency for the controlled truck. The oxidative potential of the emitted PM, measured by means of the dithiothreitol (DTT) assay, showed reductions with the use of biodiesel blends relative to CARB ULSD for the uncontrolled truck. Overall, the cellular responses to the particles from each fuel were reflective of the chemical content, i.e., particles from CARB ULSD were the most reactive and exhibited the highest cellular responses.