A modified version of the multi-dimensional KIVA-II code is used to model the effects of multiple injection schemes and exhaust gas recirculation (EGR) on direct injected diesel engine NOx and soot emissions. The computational results, which also considered double and triple injection schemes and varying EGR amounts, are compared with experimental data obtained from a single cylinder version of a Caterpillar heavy-duty truck engine. The study is done at high load (75% of peak torque at 1600 rpm) where EGR is known to produce unacceptable increases in soot (particulate). The effect of soot and spray model formulations are considered. This includes a new spray model based on Rayleigh-Taylor instabilities for liquid breakup. A soot oxidation model that accounts for turbulent mixing and kinetic effects were found to give accurate results. The results showed excellent agreement between predicted and measured in-cylinder pressure, and heat release data for the various cases. In addition, the results showed relatively good agreement between measured and predicted engine-out NOx and soot emissions. The study confirms the benefit of combining EGR and multiple injection, previously seen experimentally, as a potential means to control both NOx and soot emissions simultaneously. Although EGR is effective at reducing NOx by lowering peak in-cylinder temperatures, there is a substantial trade-off in increased soot emissions due to increased high temperature rich regions. By using multiple injection, the amount of soot formed in these regions is reduced considerably. Multiple injection schemes improves fuel-air mixing and leans out the in-cylinder mixture, thus reducing the high soot forming regions. The present work further demonstrates the usefulness of multi-dimensional modeling as a tool in designing low emission diesel engines and as a way to gain greater insight into in-cylinder events.