A new multi-zone model for the simulation of HCCI engine is here presented. The model includes laminar and turbulent diffusion and conduction exchange between the zones and the last improvements on the numerical aspects. Furthermore, a new strategy for the zone discretization is presented, which allows a better description of the near-wall zones. The aim of the work is to provide a fast and reliable model for carrying out chemical analysis with detailed kinetic schemes. A preliminary sensitivity analysis allows to verify that 10 zones are a convenient number for a good compromise between the computational effort and the description accuracy. The multi-zone predictions are then compared with the CFD ones to find the effective turbulence parameters, with the aim to describe the near-wall phenomena, both in a reactive and non-reactive cases. Finally, the model is validated against experimental data of HCCI combustion of fossil and bio-fuels (n-heptane, methyl-hexanoate, and methyl-decanote).