The purpose of this study was to measure the impact of various sources of petroleum-based and bio-based diesel fuels on regulated emissions and fuel economy in diesel particulate filter (DPF) equipped diesel engines. Two model year 2008 diesel engines were tested with nine fuels including a certification ultra-low sulfur diesel (ULSD), local ULSD, high aromatic ULSD, low aromatic ULSD, and twenty percent blends of biodiesel derived from algae, camelina, soy, tallow, and yellow grease. Regulated emissions were measured over the heavy duty diesel transient test cycle. Measurements were also made of DPF-out particle size distribution and total particle count from a 13-mode steady state test using a fast mobility particle sizer. Test engines were a 2008 Cummins ISB and a 2008 International Maxx Force 10, both equipped with actively regenerated DPFs. Fuel consumption was roughly 2% greater over the transient test cycle for the B20 blends versus certification ULSD in both engines, consistent with the slightly lower energy content of biodiesel. Unlike studies conducted on older model engines, these engines equipped with diesel oxidation catalysts and DPFs showed small or no measurable fuel effect on the tailpipe emissions of total hydrocarbons (THC), carbon monoxide (CO) and particulate matter (PM). No differences in particle size distribution or total particle count were seen in a comparison of certification ULSD and B20 soy, with the exception of engine idling conditions where B20 produced a small reduction in the number of nucleation mode particles. In the Cummins engine, B20 prepared from algae, camelina, soy, and tallow resulted in an approximately 2.5% increase in nitrogen oxides (NOx) compared to the base fuel. The International engine demonstrated a higher degree of variability for NOx emissions, and fuel effects could not be resolved (p > 0.05). The group of petroleum diesel test fuels produced a range of NOx emissions very similar to that caused by blending of biodiesel. Test cycles where an active regeneration of the DPF occurred resulted in a nearly threefold increase in NOx emissions and a 15% increase in fuel consumption. The full quantification of DPF regeneration events further complicates the accurate calculation of fuel impacts on emissions and fuel consumption.