Despite the fact that HCCI engines are distinguished by mixture homogeneity, some degree of stratification always appears inside a combustion chamber. It is especially applied to residual effect engines utilizing negative valve overlap. Mixture stratification is a result of the imperfect mixing of fresh air with trapped residuals. Direct fuel injection introduces stratification as well, due to fuel vaporization. As a consequence, the temperature within the combustion chamber is uneven. Thermal stratification affects auto-ignition timing and combustion evolution in a high extent. The purpose of this study was to evaluate a degree of thermal stratification in HCCI engine utilizing negative valve overlap. Investigations were performed using three-dimensional CFD model of the combustion system, made by using AVL FIRE software. Simulations were realized for various timings of fuel injection into the cylinder. It was found that fuel injection timing had a significant effect on the thermal stratification and resulting auto-ignition timing.