The main objective of the present work is to make a computational study of stratified scavenging system in two-stroke medium capacity engines to reduce or to curb the emissions from the two-stroke engines. The 3-D flows within the cylinder are simulated using computational fluid dynamics and the code Fluent 6. Flow structures in the transfer ports and the exhaust port are predicted without the stratification and with the stratification, and are well predicted. The total pressure and velocity map from computation provided comprehensive information on the scavenging and stratification phenomenon. Analysis is carried out for the transfer ports flow and the extra port in the transfer port along with the exhaust port when the piston is moving from the top dead center to the bottom dead center, as the ports are closed, half open, three forth open, and full port opening. An unstructured cell is adopted for meshing the geometry created in CATIA software. Flow is simulated by solving governing equations namely conservation of mass momentum and energy using SIMPLE algorithm. Turbulence is modeled by high Reynolds number version k-e model. Experimental measurements are made for validating the numerical prediction. Good agreement is observed between predicted result and experimental data; that the stratification had significantly reduced the emissions and fuel economy is achieved.