This work presents an experimental analysis which is carried out to study the instantaneous heat fluxes, during the engine cycle, in the cylinder head and exhaust manifold of a direct injection, air-cooled, four-stroke diesel engine. For temperature measurements, a new pre-amplification unit for fast response thermocouples, appropriate heat flux sensors and an innovative, object-oriented, control code for fast data acquisition have been designed and developed at the authors＇ laboratory. The experimental installation separates the engine transient temperature signals into two parts; namely the ＇long＇- and the ＇short＇-term response ones; followed by their discrete processing in two independent data acquisition systems. One-dimensional heat conduction with Fourier analysis of the raw temperature data are implemented in order to calculate the instantaneous engine combustion chamber and exhaust pipe heat fluxes. This study concentrates on the correct interpretation of the measured temporal variations of heat fluxes and the examination of the effect of engine load and speed on the cylinder head and exhaust manifold heat flux losses. Many interesting aspects of transient engine heat transfer are revealed. The simultaneous presentation of heat fluxes on the cylinder head and exhaust manifold, together with the engine indicator diagram, sheds light into the mechanisms governing transient heat transfer during an engine cycle.