The study presents interesting investigations regarding the gas mixture homogeneity in HCCI linear engines. A 3D-CFD model has been employed to simulate the gas exchange process and another 1D chemical kinetics model has been used to simulate the combustion process in the engine model. The gas mixture homogeneity has been quantified and examined using a defined uniformity index found in the literature. The uniformity of both fuel and residual gas have been considered in evaluating the uniformity index. Different engine parameters including the intake pressure and temperature and the engine frequency have been investigated by evaluating their effect on the gas mixture homogeneity. The results show that some parameters have a significant effect on the mixture homogeneity when they compared to other parameters. High intake pressure can disturb the gas mixture homogeneity by decreasing the fuel concentration in the cylinder and pushing the residual gas toward the crevice region. On the other hand, at high engine frequency; the mixture volume based homogeneity index is less than this at low engine frequency. The engine intake temperature seems to have no significant effect on the homogeneity of both fuel and the residual gas within the combustion chamber. The study includes also a comparison between the effect of each parameter on the gas mixture species at the cylinder boundaries where the heat loss to ambient occurs. The species at the boundaries vary in their concentration and uniformity but with different magnitudes for each engine parameter. In terms of the uniformity, the gas mixture at the boundaries is not affected by changing the engine intake temperature and operation frequency but it is influenced by the intake pressure significantly. On the other hand, the gas mixture mass fraction at the boundaries is strongly affected by the intake pressure and the engine frequency as they influence the species transfer within the engine much more than the intake temperature.