Temperature stratification plays an important role in HCCI combustion. The onsets of auto-ignition and combustion duration are sensitive to the temperature field in the engine cylinder. Numerical simulations of HCCI engine combustion are affected by the use of wall boundary conditions, especially the temperature condition at the cylinder and piston walls. This paper reports on numerical studies and experiments of the temperature field in an optical experimental engine in motored run conditions aiming at improved understanding of the evolution of temperature stratification in the cylinder. The simulations were based on Large-Eddy-Simulation approach which resolves the unsteady energetic large eddy and large scale swirl and tumble structures. Two dimensional temperature experiments were carried out using laser induced phosphorescence with thermographic phosphors seeded to the gas in the cylinder. The results revealed different mechanisms for the development of temperature stratification: intake gas and residual gas mixing, heat transfer in the wall boundary layer, compression of the charge, and large scale flow transport. The sensitivity of LES results to different wall boundary conditions and inflow conditions was analyzed.