A three-dimensional reacting flow modeling approach is presented for predictions of compression ignition, combustion, NOx and soot emissions over a wide range of operating conditions in a diesel engine. The ignition/combustion model is based on a modified eddy dissipation concept (EDC) which has been implemented into the KIVA-3V engine simulation code. The modified EDC model is used to represent the thin sub-grid level reaction zone and the small scale molecular mixing processes. In addition, a realistic transition model based on the local normalized fuel mass fraction is implemented to shift from ignition to combustion. The modified EDC model is combined with skeletal n-heptane chemistry and a soot dynamics model, which includes nucleation, surface growth and oxidation and coagulation processes. The NO formation and destruction processes are based on the extended Zeldovich reaction mechanism. The modeling results are calibrated against experimental engine data taken at benchmark conditions. The model is subsequently used to conduct parametric studies of the effects of injection timing and exhaust gas recirculation (EGR) on engine combustion and emissions. Predictions of cylinder pressure traces and heat release rates are in very good agreement with the experimental data (e.g., pressure predictions within 3 bar of the experimental data) for a range of injection timings, EGR rates and speeds. The experimental trends observed for the soot and NO emissions are also reproduced by the modeling results. Overall, the modeling approach demonstrates promising predictive capabilities at reasonable computational costs.