Hydrotreated Vegetable Oil (HVO) and Sugar-to-Diesel as next-generation bio diesel fuels consist of normal and iso-paraffin, and those carbon number of paraffinic hydrocarbons and distillation characteristics are narrow distribution. These characteristics would cause to deteriorate the evaporation and mixture with air and fuel. Therefore, in this study, the effects of normal paraffin (Tridecane) and iso-paraffin (HVO) on emission characteristics and cold start performance in a diesel engine were investigated by engine dynamometer tests, cold start vehicle tests, and spray analyzer tests. From the results, it was found that normal and iso-paraffin are beneficial for HC, CO, Smoke emission reduction. In addition, isomerization is effective for the diesel engine to fulfill cold start performance, since normal paraffin of narrow carbon number distribution became solidified under low temperature and high pressure condition in a common rail system.