To control auto-ignition timing in a Homogeneous Charge Compression Ignition (HCCI) engine, it is essential to be able to predict the auto-ignition timing. Since charge properties influence the auto-ignition timing, a control-oriented model is further developed to predict the HCCI auto-ignition timing and the sensitivity to the charge properties is examined. The simulation results show that in the studied range the Start of Combustion (SOC) is the most sensitive to the variation of charge temperature and the least sensitive to the variation of Exhaust Gas Recirculation (EGR) rate and the sensitivity to charge temperature increases with decreasing EGR rate.