A compact diesel-powered generator (5 kW) experimental setup was used to systematically evaluate the emissions generated by the combustion of several commercially produced alternative diesel fuels. The measured diesel engine exhaust components include oxides of nitrogen (NOx), carbon monoxide (CO), particulate matter (PM), volatile hydrocarbons (HCs), and carbon dioxide (CO2). Alternative diesel fuels, including biodiesel made from various feedstocks (soy, canola, palm, and tallow) and gas-to-liquid (GTL) diesel fuel, were compared to Texas low-emission diesel (TxLED), a petroleum-based ultra-low sulfur diesel (ULSD), in terms of emissions and fuel consumption. The biodiesel feedstock oil identity is an important variable affecting the level of NOx emissions, because increases were found for soy biodiesel and canola biodiesel, which are the most common feedstocks in the United States and Europe, respectively. At low engine load, NOx emissions increased for all biodiesels when compared to the ULSD, with the soy-based fuel giving the largest increase, followed by canola-based fuel and then tallow-based fuel, with palm-based biodiesel producing the smallest increase in NOx. At high engine load, NOx emissions for biodiesels followed the same relative ranking, but the increases were smaller for biodiesel made from the soy and canola feedstocks and decreases were observed for palm and tallow-based biodiesel. NOx emissions for the GTL decreased at both low and high load. Emissions of CO and HCs decreased for all alternative diesel fuels at both load points. Quantification of several exhaust HC species was accomplished, with the highest concentrations belonging to ethene, pentane, formaldehyde, and acetaldehyde. Biodiesels produced slightly more CO2 compared to ULSD, while GTL produced slightly less. The small differences in CO2 emissions were attributed to the carbon/hydrogen (C/H) ratio of the fuels and to the conversion of CO, HCs, and PM to CO2. This study provides further evidence that alternative diesel fuels can be used in compression ignition engines designed for conventional diesel without modification and that emission reductions can be achieved in some cases.