In this work, heat loss was investigated in two different HCCI single cylinder engines. Thermocouples were adapted to the surfaces of the cylinder heads and the temperature oscillations were detected in a wide range of the engine operation maps. The resultant heat transfer profiles were compared to the heat losses predicted by existing models. As major discrepancies were stated, a new phenomenological model was developed that is well-manageable and describes the heat loss in HCCI mode more precisely than existing models.To analyze the insulating effect of deposits, the heat transfer equation was solved analytically by an approach that allows consideration of multiple layers with different material properties and thickness. This approach was used for the first time in conjunction with engines to calculate the heat flux at the surface of deposits and the deposit thickness. Additionally, the heat loss measured in HCCI operation was compared to the heat loss detected in homogeneous SI operation in the same engine. The differences in the heat transfer characteristics are demonstrated.