In the present study, engine tests were conducted on a modified single cylinder four stroke compression ignition (CI) engine operated in homogeneous charge compression ignition (HCCI) mode with injection of diesel and biodiesels through intake manifold. The intake air temperature varied from 50 to 80 °C for diesel and 55 to 85 °C for biodiesel using air pre heater. The coolant temperature varied from 40 to 60 °C for both the diesel and biodiesel operation. For the comparison purpose, CI engine fuelled with diesel was operated at the injection timing of 23°BTDC and an injector pressure of 205 bar. It is seen that HCCI mode of engine operation with diesel and biodiesel resulted into 35-45% lower brake thermal efficiency (BTE) with significant reduction in nitrogen oxide (NOx) emission by 98% and smoke emissions by 65-75%. On the other hand, HCCI engine operation with diesel and biodiesels showed increased hydrocarbon (HC) emissions by 20-25 times and carbon monoxide (CO) emissions by 30-40%. However, peak pressure (PP) and heat release rate (HRR) decreased by 20-25% when compared to CI mode of engine operation.