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A 1-D thermo-fluid dynamic simulation code, including a quasi-D combustion model coupled with a detailed kinetic scheme, is used to analyze the combustion process in HCCI engines. The chemical mechanism has previously been validated in comparison with experimental data over a wide range of operating conditions. To explore the impact on model predictions, the cylinder was divided into multiple zones to characterize the conditions of the in-cylinder charge. Particular attention is devoted to the numerical algorithm in order to ensure the robustness and efficiency of the large system solution. This numerical model allows study of the autoignition of the air fuel mixture and determines the chemical evolution of the system. The proposed model was compared with in-cylinder temperature and chemical species profiles. The experimental activity was carried out in the combustion chamber of a single cylinder air cooled engine operating in HCCI mode.