Diesel engines are widely used in almost all walks of life and cannot be dispensed with in the near future, and common rail technology is now widely applied in diesel engines for its advantages. An experimental investigation is carried out to establish the emission characteristics of a common rail diesel engine fuelled with diesel and biodiesel produced from cottonseed oil. The emissions measured were carbon monoxide, hydrocarbon, oxides of nitrogen and smoke. From the results, it is found that most exhaust emissions encountered with conventional diesel fuel are reduced with biodiesel fuel, with the exception of nitrogen oxides. From the investigation it can be concluded that biodiesel can be used as an alternative to diesel in a common rail diesel engine without any engine modifications.