A computational methodology has been developed for loss prediction in intake regions of internal combustion engines. The methodology consists of a hierarchy of four major tasks: (1) proper computational modeling of flow physics; (2) exact geometry and high quality and generation; (3) discretization schemes for low numerical viscosity; and (4) higher order turbulence modeling. Only when these four tasks are dealt with properly will a computational simulation yield consistently accurate results. This methodology, which is has been successfully tested and validated against benchmark quality data for a wide variety of complex 2-D and 3-D laminar and turbulent flow situations, is applied here to a loss prediction problem from industry. Total pressure losses in the intake region (inlet duct, manifold, plenum, ports, valves, and cylinder) of a Caterpillar diesel engine are predicted computationally and compared to experimental data. Detailed documentation is provided for the location of loss pockets, mechanisms responsible for losses, and the relative magnitude of different loss sources. Large scale, 3-D, viscous, turbulent flow simulations were carried out for low, medium, and high valve lift cases using up to 840,000 unstructured/adaptive tetrahedral grid cells and the complete form of the time-averaged Navier-Stokes equations. Good agreement was found between predicted and measured results.