A modified version of KIVA-II code is applied to scavenging flow simulation of a four-poppet-valved two-stroke engine. The standard k-ε turbulence model is used with no slip on the wall. Grid is generated through direct interface with three dimensional CAD data using a commercial CAE package. Valve motion is taken into account by identifying the cells occupied by the valve structure and putting them as solid obstacle cells. Results show reasonable trends for variation of the velocity field and fresh air mass fraction distribution with crank angle. Parametric study shows that the intake port orientation does not have much effect on the cylinder flow and scavenging efficiency due to strong flow diversion by the valves.