This study explores the diesel injection and combustion processes in an effort to better understand the differences in NOx emissions between biodiesel, Fischer−Tropsch (FT) diesel, and their blends with a conventional diesel fuel. Emissions studies were performed with each fuel at a variety of static fuel injection timing conditions in a single-cylinder DI diesel engine with a mechanically controlled, in-line, pump-line-nozzle fuel injection system. The dynamic start of injection (SOI) timing correlated well with bulk modulus measurements made on the fuel blends. The high bulk modulus of soy-derived biodiesel blends produced an advance in SOI timing compared to conventional diesel fuel of up to 1.1 crank angle degrees, and the lower bulk modulus of the FT diesel produced a delay in SOI timing of up to 2.4 crank angle degrees. Compared to conventional diesel fuel at high load, biodiesel fuel blends produced increases in NOx emissions of 6−9% while FT fuels caused NOx emissions to decrease 21−22%. Shifts in fuel injection timing, caused by bulk modulus differences, were largely responsible for the NOx increases, but pure FT diesel produced lower NOx emissions than expected on the basis of SOI alone. Further analysis showed that no trends were seen between NOx and either ignition delay or maximum cylinder temperature, and only weak, or fuel-specific, relationships were seen between NOx and maximum heat release rate and the timing of maximum heat release rate. The timing of the maximum cylinder temperature, however, did produce a relationship with NOx emissions that was not dependent on fuel type.