In view of ever increasing demands imposed on internal combustion engines, particularly regarding the lowering of harmful emissions and fuel consumption, common combustion processes are being improved and new ones are being developed. One of newly developed processes, i.e. the Homogeneous Charge Compression Ignition combustion (HCCI), is the subject of this paper. In order to give a contribution to a further development of the process, a new, multi zone combustion model of the HCCI process has been developed. The model is classified as a so-called zero dimensional model due to its approach to the problem. The in-cylinder diversity is simulated by a larger number of zones in which different conditions are calculated. Since the model is based on thermodynamic and chemical kinetic equations, it can be considered as a thermo-kinetic model. In addition to chemical kinetics, the model also involves the heat transfer between zones in contact, as well as the heat transfer between boundary zones and the cylinder walls. Since the system of differential equations includes all the zones simultaneously, there is no need for the correction of the obtained results. The model also includes the mass transfer between the zones, which is modelled by a timeless model, developed for this particular purpose. The testing of the model has shown that it can be used in different ways. On the one hand, it can be used for the calculation of general physical properties of the cylinder, such as changes in pressure, temperature and the rate of heat release, etc. These properties can be very accurately calculated in the entire operating window of the HCCI engine without a special adjustment of the model constants. On the other hand, the model can calculate harmful emissions of the engine. By examining the changes in mass fractions of species in each zone, the sources of these emissions and the possibilities of emission reductions can be analyzed. Although the calculation accuracy of emissions is rather good even without the adjustment of the model constants, the accuracy of the calculation can be further improved by adjusting them. A further analysis of the results has shown that a future development of this calculation model should include an increased number of zones together with the development of a heat transfer model and the modelling of calculation constants.