The effects of a zeolite urea-selective catalytic reduction (SCR) aftertreatment system on a comprehensive spectrum of chemical species from diesel engine emissions were investigated in this study. Representative samples were collected with a newly developed source dilution sampling system after an aging process designed to simulate atmospheric dilution and cooling conditions. Samples were analyzed with established procedures and compared between the measurements taken from a baseline heavy-duty diesel engine and also from the same engine equipped with the exhaust aftertreatment system. The results have shown significant reductions for nitrogen oxides (NOx), carbon monoxide, total hydrocarbons, polycyclic aromatic hydrocarbons (PAHs), and organic carbon (OC) emissions. Additionally, less significant yet notable reductions were observed for particulate matter mass and metals emissions. Furthermore, the production of new species was not observed with the addition of the zeolite urea-SCR system joined with a downstream oxidation catalyst.