A multidimensional computational method is employed to investigate the details of the in-cylinder flow and gas exchange process in a loop-scavenged two-stroke cycle spark-ignition engine. The engine geometric compression ratio is 15:1 and the study pertains to the operating condition of 5000 rpm.The inlet and outlet boundary conditions (c.f. the instantaneous thermodynamic properties and the intake and exhaust mass flow rates) were obtained from a gas dynamic calculation procedure. This enabled incorporation of the effect of the pressure waves causing strong flow oscillations in the scavenge and exhaust ports.The results reveal that the in-cylinder flow structure established early during the scavenge phase comprises of a three-dimensional loop and a pair of toroidal vortices. This vortex structure is responsible for impairment of the scavenging efficiency. The flow structure was found to be sensitive to the details of the scavenge system layout. The occurence of ‘reverse’ flows through the scavenge and exhaust ports, caused by pressure wave oscillations in the port system, markedly affects the in-cylinder flow structure and mixing process. Furthermore it was found that the isothermal model of scavenging characterization is inadequate for engine operating conditions.