The objective of this research was to develop a detailed numerical spray atomization, ignition, and combustion model for direct-injection diesel engines using KIVA3V code that could be applied to biodiesel fuels for investigating NO, emissions. Several modified or recalibrated submodels were incorporated into KIVA3V including a KH-RT spray breakup model, a Shell ignition model, and a single-step kinetic combustion model. This modified model was applied to a John Deere 4045T direct-injection diesel engine fueled by a soybean methyl ester a yellow grease methyl ester and No. 2 diesel fuel. The output of the model was in close agreement with the experimental. measurements of cylinder pressure and heat release rate from this engine. It was predicted from the modeling results that the two biodiesel fuels had shorter ignition delay and higher overall cylinder temperatures than diesel fuel. The in-cylinder spray analysis indicated that the soybean methyl ester had slightly longer penetration than diesel fuel, but the yellow grease methyl ester had shorter penetration than diesel fuel. Fewer particle numbers were predicted for the two biodiesel fuels. Both soybean methyl ester and yellow grease methyl ester had more widespread high-temperature distribution areas than diesel fuel, which could account for the increases in NOx emissions typically measured for biodiesel fuels.