Selective catalytic reduction (SCR) systems are in use on heavy duty diesel engines for NOx control. An SCR NOx reduction efficiency of higher than 95% is required to meet the proposed increasingly stringent NOx emission standards and the 2014-2018 fuel consumption regulations. The complex engine exhaust conditions including the nonuniformity of temperature, flow, and maldistribution of NH3 present at the catalyst inlet need to be considered for improved performance of the SCR system. These factors cause the SCR to underperform negatively impacting the NOx reduction efficiency as well as the NH3 slip.In this study, the effects of the nonuniformity of temperature, flow velocity and maldistribution of NH3 on the SCR performance were investigated using 1-dimensional (1D) model simulations for a Cu-zeolite SCR. The model was previously calibrated and validated to reactor and steady-state and transient engine experimental data. The SCR engine experimental measurements collected from a transient cycle were used as the baseline for the simulations. The model was configured to include multiple axial channels running in parallel. Different inputs were assigned to the channels of the model to simulate the catalyst inlet nonuniformity. Another important factor affecting the SCR performance is the inlet NO2/NOx ratio. Its effects on the SCR NOx reduction, NH3 slip and NH3 storage under transient conditions were investigated using simulations from a single-channel version of the same model. It was determined that the SCR inlet NH3 maldistribution caused a 3.5% decrease in NOx reduction efficiency over a surrogate HD-FTP cycle. The nonuniformity of the SCR inlet temperature and exhaust mass flow rate had minimal effect on the cycle cumulative NOx reduction (<1%). Controlling the inlet NO2/NOx ratio to near 0.5 is important to achieve the optimal SCR performance.