This study evaluated the effects of various combinations of fuels and emission control technologies on exhaust emissions from a heavy-duty diesel engine tested on an engine dynamometer. Ten fuels were studied in twenty four combinations of fuel and emission control technology configurations. Emission control systems evaluated were diesel oxidation catalyst (DOC), continuously regenerating diesel particulate filter (CRDPF), and the CRDPF coupled with an exhaust gas recirculation system (EGRT). The effects of fuel type and emission control technology on emissions of benzene, toluene, ethylbenzene, xylene (BTEX), and 1,3-butadiene, elemental carbon and organic carbon (EC/OC), carbonyls, polycyclic aromatic hydrocarbons (PAHs), and nitro-PAHs (n-PAHs) are presented in this paper. Regulated gaseous criteria pollutants of total hydrocarbons (THC), carbon monoxide (CO), oxides of nitrogen (NOx) and particulate matter (PM) emissions have been reported elsewhere. In general, individual unregulated emission with a CRDPF or an EGRT system is similar (at very low emission level) or much lower than that operating solely with a DOC and choosing a “best” fuel. The water emulsion PuriNOx fuel exhibited higher BTEX, carbonyls and PAHs emissions compared to other ultralow sulfur diesel (ULSD) fuels tested in this study while n-PAH emissions were comparable to that from other ULSD fuels. Naphthalene accounted for greater than 50% of the total PAH emissions in this study and there was no significant increase of n-PAHs with the usage of CRDPF.