The New York State Department of Environmental Conservation (DEC) and Environment Canada have jointly participated along with partners the New York City Metropolitan Transit Agency (MTA); Johnson Matthey, Environmental Catalysts & Technologies; Equilon Enterprises, LLC and Corning, Inc. in a project to evaluate the effect of various combinations of fuels and aftertreatment configurations on diesel emissions. Emissions measurements were performed during engine dynamometer testing of an International DT 466E heavy-duty diesel engine. Fuels tested in the study were Diesel Fuel 1 and 2, low sulfur diesel (150 ppm), two ultralow sulfur fuels (<30 ppm), Fischer-Tropsch, Biodiesel, PuriNOx™ and two Ethanol-Diesel blends. Configurations tested were: engine out, and diesel oxidation catalyst, continuously regenerating diesel filter, and exhaust gas recirculation aftertreatment. In general, the use of more aggressive aftertreatment (ie. DOC vs engine out, CRDPF vs DOC, etc) had a much more significant effect on emissions of PM, NOx, NO, HC and CO than the use of non-standard fuels, including the blended fuels. EGR-DPF was the only after treatment technology that significantly affected NOx emissions, reducing them an average of 42% from the DOC case for all fuels. NOx was reduced 41% from the Engine Out case for EULSD, the only fuel that was tested with both configurations. The only exception to this general trend was that PNOx fuel produced similar NOx emissions in the DOC configuration to the use of EGR-DPF after treatment with the ultralow sulfur fuels.