It seems very difficult to comply with upcoming stringent emission standards in vehicles. To develop low emission engines, better quality of automotive fuels must be achieved. Since sulfur contents in diesel fuels are transformed to sulfate-laden particulate matters as a catalyst is applied, it is necessary to provide low sulfur fuels before any Pt-based oxidation catalysts are applied. In general, flash point, distillation $90\%$ and cetane index are improved but viscosity can be worse in the process of desulfurization of diesel fuel. Excessive reduction of sulfur may cause to degrade viscosity of fuels and engine performance in fuel injection systems. This research focused on the performance of an 11,000 cc diesel engine and emission characteristics by the introduction of ULSD, bio-diesel and a diesel oxidation catalyst, where the bio-diesel was used to improve viscosity of fuels in fuel injection systems as fuel additives or alternative fuels.