The focus of the present study is to investigate the importance of mass transfer on the formation of the most important HCCI engine emissions, i.e. unburned HC and CO emissions. A multi-zone model is used for this purpose. The multi-zone model includes sub-models for the heat transfer between zones and to the cylinder wall and for the mass transfer between the hotter and colder regions of the combustion chamber. The combustion mechanism is modeled using a reduced set of chemical reactions coupled with a chemical kinetics solver. The results indicate that mass transfer during combustion and expansion plays a significant role on the formation of both the unburned HC and the CO emissions and therefore must be taken into account for the closed part of the engine cycle, i.e. compression, combustion and expansion. According to the model results, the formation of these emissions is located mainly at the crevice and the near-the-wall regions and is determined by the temperature field and mass transfer. It is shown that neglecting mass transfer in these regions during combustion and expansion would result to a significant deviation from the values predicted with the inclusion of mass transfer. (C) 2008 Elsevier Ltd. All rights reserved.