New measurements have been done in order to obtain information concerning the effect of EGR and a paraffinic hydrotreated fuel for the smoke and NOx emissions of a heavy-duty diesel engine. Measured smoke number and NOx emissions are explained using detailed chemical kinetic calculations and CFD simulations. The local conditions in the research engine are analyzed by creating equivalence ratio -temperature (Phi-T) maps and analyzing the CFD results within these maps. The study uses different amount of EGR and two different diesel fuels; standard EN590 diesel fuel anda paraffinic hydrotreated vegetable oil (HVO). The detailed chemical kinetic calculations take into account the different EGR rates and the properties of the fuels. The residence time in the kinetical calculations is used to explain sooting combustion behavior within diesel combustion. It was observed that NOx emission trends can be well captured with the Phi-T maps but the situation is more difficult with the engine smoke.