High material throughput of state of the art combine harvesters and raising quantity of non-conventional separation systems lead to an increased load for the cleaning shoe. In addition to the mechanical part, the separation success depends largely on the pneumatic decompaction. Computational fluid dynamics (CFD) is used to determine the distribution of air volume flow to individual functional elements (cascades and chaffer/sieve) as well as the distribution of air velocity along chaffer and sieve. The methods to include the chaffer and the air flow resistance of material layer are presented and discussed. The computational results confirm the experience of unfavorable flow conditions in case of loaded cleaning shoe and are used to evaluate the effect of design modifications.