Due to compressibility, reactivity, evaporation and mixing, the gas species concentration varies significantly along the intake and exhaust pipes of an engine. An understanding of this behavior is vital to correctly predict catalyst performance because the behavior of a catalyst very much depends on the instantaneous local species concentrations, rather than those in the cylinder. Also, knowing this behavior is more important to assess the effects of exhaust gas recirculation (EGR). The objective of this research is to develop a tool that is capable of predicting the instantaneous species concentration throughout the entire intake and exhaust system, and to lay out a foundation to model catalysts in the near future. This is done by first developing a complete engine cycle simulation model that is able to accurately predict wave dynamics in the piping system. Then, species tracking is accomplished by solving the species conservation equations. The twelve species formed due to combustion commonly seen in engine applications are studied. Comparisons with experimental data using the current model are made, and reasonable agreements are obtained.