An in-cylinder charge exchange process in a gasoline homogeneous charge compression ignition (HCCI) engine operated in a negative valve overlap (NVO) mode was studied. Research was performed using a single-cylinder research engine with fully variable valve actuation. Combination of in-cylinder pressure traces processing and fluid flow model enables cycle-by-cycle analysis of charge composition and temperature. It allows forecasting of in cylinder pressure volume and temperature-volume histories and can be used for physical-based engine control. In this paper influence of valves timings and valves lifts on the gas exchange process was analyzed. Special attention was paid to the effects of backflows of the in cylinder charge to an intake port.