The focus of the present study is to assess the effect of mass transfer on the formation of unburned HC and CO emissions in HCCI engines. A multi-zone model was modified and used for this purpose. The new feature of the multi-zone model is its ability to switch between two distinct simulation modes, i.e. either including or excluding mass transfer between zones. The switch between modes occurs at a user-defined point in the engine closed cycle. Apart from mass transfer, the two modes use identical sub-models for the heat transfer between zones and to the cylinder wall and for combustion simulation, which is modeled using a reduced set of chemical reactions coupled with a chemical kinetics solver. Using the modified multi-zone model, four cases were simulated and compared: one including mass transfer throughout the closed cycle, and three cases whereby mass transfer is neglected after the initiation of the 1st or 2nd heat release or after the completion of main heat release. The simulation results reveal that mass transfer affects the HC and CO accumulated at the colder regions during combustion and governs the HC partial oxidation and CO production during expansion. For the operating conditions studied, neglecting mass transfer during combustion results to an underprediction of HC by as much as 50% and of CO by 45% relative to the case where mass transfer is considered for. Omitting mass transfer only during expansion, results to an overestimation of HC by 9% and to an underestimation of CO by 26%. (C) 2009 Elsevier Ltd. All rights reserved.