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Adjusting the Residual Gas Fraction (RGF) by means of Variable Valve Actuation (VVA) is a strong candidate for controlling the ignition timing in Homogeneous Charge Compression Ignition (HCCI) engines. However, at high levels of residual gas fraction, insufficient mixing can lead to the presence of considerable temperature and composition variations. This paper extends previous modeling efforts to include the effect of RGF distribution on the onset of ignition and the rate of combustion using a multi-dimensional fluid mechanics code (KIVA-3V) sequentially with a multi-zone code with detailed chemical kinetics. KIVA-3V is used to simulate the gas exchange processes, while the multi-zone code computes the combustion event. It is shown that under certain conditions the effect of composition stratification is significant and cannot be captured by a single-zone model or a multi-zone model using only temperature zones.