Computational fluid dynamics methods are applied to the intake regions of a diesel engine in the design stage at Caterpillar. Using a complete, tested and validated computational methodology, fully viscous 3-D turbulent flow simulations are performed for three valve lifts, with the goal of identifying and understanding the physics underlying loss in the intake regions of IC engines. The results of these simulations lead to several design improvements in the intake region. These improvements are made to the computational domain, and flow simulations are again performed at three different valve lifts. Improvements in overall total pressure loss of between 5% and 33% are found in the computed results between the original and modified (improved) domains. Physical mechanisms responsible for these improvements are documented in detail.