This article is a comparative study of use of mineral diesel and biodiesel derived from cotton seed oil of Pakistani origin. The main problems associated with biodiesel are, its very high viscosity and specific gravity, which are due to long chain triglyceride esters with free fatty acids. The esters are converted into simple structure mono-glyceride esters via transesterification process. The experiments were carried out using blends of diesel and biodiesel with different ratios, to investigate the performance characteristics of engine and exhaust emissions. The experimental results show that the engine using B100 resulting in about 10% higher brake specific fuel consumption and about 10% lower brake thermal efficiency as compared to the use of B0. The engine emissions were almost free from SOx , having reduced amount of CO, CO2, and THC, but having higher amount of NOx , when B100 was used as fuel. The fuel is becoming more popular due to the reduction in nasty pollutant emissions.