Particulate matter in diesel engine exhaust, particularly nano-particles, can cause serious human health problems including diseases such as lung cancer. Because diesel nano-particle issues are of global concern, regulations on particulate matter emissions specify that not only the weight of particulate matter emitted but also the concentration of nanoparticles must be controlled. This study aimed to determine the effects on nano-particle and PM emissions from a diesel engine when applying a urea-SCR system for NOx reduction. We found that PM weight increases by approximately 90% when urea is injected in ND-13 mode over the emission without urea injection. Additionally, PM weight increases as the NH3/NOx mole ratio is increased at 250 °C. In SEM scans of the collected PM, spherical particles were observed during urea injection, with sizes of approximately 200 nm to 1 μm. This study was designed to determine the conditions under which nano-particles and PM are formed in a urea-SCR system and to relate these conditions to particle size and shape via a quantitative analysis in ND-13 mode.