A new six-zone simulation model for the calculation of changes in an HCCI engine has been developed and tested. The model uses comprehensive chemical kinetics and a non-sequential solver of zone states. This means that the state vector comprises the states in all zones, and that the changes in states in all zones are calculated simultaneously. In this manner, physical accuracy during the calculation of a new state is maintained at the expense of the calculation time. The model comprises the wall heat transfer, zone heat transfer and zone mass transfer as means of zone interactions. The cylinder is divided into two central zones, three boundary layer zones and one crevice zone. Since the model calculates only the high pressure part of an engine cycle, it has been connected with the cycle simulation software AVL Boost. In this way, a relatively easy-to-use, higher accuracy, simulation tool for HCCI engines has been obtained. The model was tested by comparing simulation results with experimental ones. The comparison was made with a single cylinder engine running on isooctane. The calculated pressure and net rate of heat release correspond to the experimental results very well in the entire operating region. By using the six-zone simulation model, a big improvement, compared to the single zone simulation, is obtained in operating points where combustion efficiency is over 90%. Results of emissions of unburned HC and CO show that predictions of these species are greatly improved, but it has also been noticed that these emissions are still slightly underpredicted. Predictions of emissions that come from crevice regions are good, but emissions that come from the corners of boundary layers are not captured very well. A detailed description of the simulation model is given, and validation results and possibilities of a further development are discussed.