Instantaneous heat flux measurements have shown that, in the expansion stroke, heat can flow from the wall into the combustion chamber, even though the bulk gas temperature is higher than the wall temperature. This unexpected result has been explained by modelling of the unsteady flows and heat conduction within the gas side thermal boundary layer. This modelling has shown that these unsteady effects change the phasing of the heat flux, compared with that which would be predicted by a simple convective correlation based on the bulk gas properties. Twelve fast response thermocouples have been installed throughout the combustion chamber of a pent roof, four-valve, single-cylinder spark ignition engine. Instantaneous surface temperatures and the adjacent steady reference temperatures were measured, and the surface heat fluxes were calculated for motoring and firing at different speeds, throttle settings and ignition timings. To make comparisons with these measurements, the combustion system was modelled with computational fluid dynamics (CFD). This was found to give very poor agreement with the experimental measurements, so this led to a review of the assumptions used in boundary layer modelling. The discrepancies were attributed to assumptions in the law of the wall and Reynolds analogy, so instead the energy equation was solved within the boundary layer. The one-dimensional energy conservation equation has been linearized and normalized and solved in the gas side boundary layer for a motored case. The results have been used for a parametric study, and the individual terms of the energy equation are evaluated for their contribution to the surface heat flux. It was clearly shown that the cylinder pressure changes cause a phase shift of the heat flux forward in time.