The modern Common Rail Diesel engine are, normally, optimised for being fuelled with the commercial Diesel fuel. The ECU calibrations are, consequently, defined to obtain the correct compromise between performances and emissions. It is, so, clear that if the engine is fuelled with an alternative bio-fuel with different characteristics (net heating value, stoichiometric A/F ratio, density, viscosity, etc.) the calibration must be modify. Interest in fuels from renewable sources and their use in transport has grown over the last decade. This is because of their biodegradability, potential improvements in exhaust emissions and benefits on the virtuous CO2 cycle of the earth. This paper demonstrates that it is possible to optimise the emissions and the performances of a light duty diesel C.R. engine fuelled with a vegetable derived fuel (Rapeseed Methyl-Ester) pure or blended with commercial Diesel fuel. Particularly in this paper the experimental results and the ECU control solutions referring to different fuel compositions are shown.