Rapeseed oil can be a possible substitute for fossil fuel in Diesel engines. Due to different physical properties of rapeseed oil like higher viscosity and higher compressibility compared to diesel fuel, rapeseed oil cannot be easily used in conventional Diesel engines without modifications. Especially incomplete combustion leads to deposits in the combustion chamber and higher exhaust gas emissions. These unfavorable characteristics are caused primarily by insufficient mixture preparation.The adjustment of the injection system will improve the mixture preparation and the combustion of a Diesel engine, operated with rapeseed oil. The nozzle geometry is the main parameter of the whole injection system chain to realize a better combustion process and so higher efficiency and lower exhaust gas emissions.To elaborate the effect of different nozzle geometries on the combustion behavior and exhaust gas emissions, experimental investigations using a modern single-cylinder heavy-duty engine were performed. The influence of rapeseed oil on the exhaust gas emissions was investigated and compared to analyze the interaction of a high viscous fuel like rapeseed oil with the nozzle geometry of a modern diesel injector. Since ultra-fine particles are of significant importance concerning Diesel engine emissions, analyzing the particle size distribution got special attention during these investigations.