The automobile market is, nowadays, characterized by a growing demand for cars equipped with diesel engines. This is because these offer smaller fuel consumption and better engine performance. A modern common rail turbocharged diesel engine provides performance equal to a gasoline engine, with same displacement, not turbo-charged but with a higher torque at lower engine speeds and with smaller fuel consumption. The methyl esters of vegetable oils, known as biodiesel, are receiving increasing interest because of their low environmental impact and their potential as an alternative fuel for diesel engines as they would not require any significant modification of existing engines. The modern common rail (CR) diesel engines are normally optimized for commercial diesel fuel. Consequently, the Electronic Control Unit (ECU) calibrations are defined to offer the best compromise between performance and emissions. If the engine is fuelled with an alternative fuel with different characteristics (net heating value, stoichiometric air fuel ratio (a/f), density, viscosity, etc.), it is clear that the calibration must be modified. In past experiments the authors have demonstrated that it is possible to optimize emissions and performances of a light duty CR diesel engine fueled with a vegetable derived fuel (rapeseed methyl ester) pure or blended with commercial diesel fuel, changing ECU parameters. This paper will show a detailed analysis of combustion in a modern diesel engine fueled with biodiesel and in particular some of the influences on engine parameters will be analyzed in order to demonstrate how an optimization strategy of ECU parameters could be applied to a diesel engine, when it is fueled with different fuels, with different physical/chemical characteristics.