Based on the GT-Power software, an engine cycle simulation for a biodiesel fueled direct injection compression ignition engine was developed and used to study its performance and emission characteristics. The major objectives were to establish the engine model for simulation and then apply the model to study the biodiesel fueled engine and compare it to a petroleum-fueled engine. The engine model was developed corresponding to a 4.5 liter, John Deere 4045 four-cylinder diesel engine. Submodels for flow in intake/exhaust system, fuel injection, fuel vaporization and combustion, cylinder heat transfer, and energy transfer in a turbocharging system were combined with a thermodynamic analysis of the engine to yield instantaneous in-cylinder parameters and overall engine performance and emission characteristics. At selected engine operating conditions, sensitivities of engine performance and emission on engine load/speed, injection timing, injection pressure, EGR level, and compression ratio were investigated. Variations in cylinder pressure, ignition delay, bsfc, and indicated specific nitrogen dioxide were determined for both a biodiesel fueled engine and a conventional diesel fueled engine. Cylinder pressure and indicated specific nitrogen dioxide for a diesel fueled engine were consistently higher than those for a biodiesel fueled engine, while ignition delay and bsfc had opposite trends. In addition, numerical study focusing on NOx emission were also investigated by using 5 different NO kinetics. Differences in NOx prediction between kinetics ranged from 10% to 65%.