Computational fluid dynamics simulations of the gas exchange process in a crankcase-scavenged, two-stroke engine were used to study the scavenging characteristics of the engine over the whole operating range and to investigate the effects of various design changes. The simulations used time-dependent velocity and pressure boundary conditions in the transfer and exhaust ports, respectively, which were obtained from a one-dimensional gas exchange code. The bulk flow characteristics, scavenging and trapping efficiencies, computed from these simulations compared well with experimental data. Investigation of the highest load and speed case showed that moderate port angle variations only weakly influenced the scavenging efficiency and velocity field. On the other hand, modifying the exhaust pressure to simulate single cylinder operation had a more significant effect on the scavenging and showed a possible way to control the gas exchange process.