Two methods, diesel particulate filter (DPF) and selective catalytic reduction (SCR) systems, for controlling diesel emissions have become widely used, either independently or together, for meeting increasingly stringent emissions regulations world-wide. Each of these systems is designed for the reduction of primary pollutant emissions including particulate matter (PM) for the DPF and nitrogen oxides (NOx) for the SCR. However, there have been growing concerns regarding the secondary reactions that these aftertreatment systems may promote involving unregulated species emissions. This study was performed to gain an understanding of the effects that these aftertreatment systems may have on the emission levels of a wide spectrum of chemical species found in diesel engine exhaust. Samples were extracted using a source dilution sampling system designed to collect exhaust samples representative of real-world emissions. Testing was conducted on a heavy-duty diesel engine with no aftertreatment devices to establish a baseline measurement and also on the same engine equipped first with a DPF system and then a SCR system. Each of the samples was analyzed for a wide variety of chemical species, including elemental and organic carbon, metals, ions, n-alkanes, aldehydes, and polycyclic aromatic hydrocarbons, in addition to the primary pollutants, due to the potential risks they pose to the environment and public health. The results show that the DPF and SCR systems were capable of substantially reducing PM and NOx emissions, respectively. Further, each of the systems significantly reduced the emission levels of the unregulated chemical species, while the notable formation of new chemical species was not observed. It is expected that a combination of the two systems in some future engine applications would reduce both primary and secondary emissions significantly.