An optically accessible single-cylinder high speed direct-injection (HSDI) Diesel engine was used to study the combustion process using different fuels including European low sulfur diesel and biodiesel fuels with multiple injection strategies. Influences of injection timings and fuel type on liquid fuel evolution and combustion characteristics were studied under similar loads. In-cylinder pressure was measured for heat release analysis. High-speed combustion video was also captured for all the studied cases using the same frame rate. NOx emissions were measured in the exhaust pipe. Different combustion modes including conventional diesel combustion and low-temperature combustion were confirmed from the heat release rates and the combustion images. Soot luminosity was found consistently lower for bio-diesel fuel than the European diesel fuel showing less soot emissions for all the cases. However, for NOx emissions, under conventional combustion cases, it was found that biodiesel fuel leads to increased NOx emissions. But for low-temperature combustion modes, NOx emissions were lower for bio-diesel fuel than the diesel fuel. Simultaneous reduction of NOx and soot was achieved for advanced low-temperature combustion mode.