Compression ignition (CI) engines are most efficient and robust prime movers used in transportation, power generation applications but suffer from the problems of higher level of exhaust smoke and NOx tailpipe emissions with increased use of fossil fuels. Alternative fuel that replaces diesel and at the same time that result in lower smoke and NOx emissions is presently needed. Therefore the main aim of this experimental study is to lower the smoke and NOx emissions and to use non edible oils that replace the diesel. For this locally available honge biodiesel (BHO) and cotton seed biodiesel (BCO) were selected as alternative fuels to power CI engine operated in common rail direct injection (CRDI) mode. In the first part, optimum fuel injection timing (IT) and injection pressure (IP) for maximum engine brake thermal efficiency (BTE) was obtained. In the second part, performance, combustion and emission characteristics of the CRDI engine was studied with two different fuel injectors having 6 and 7 holes each having 0.2 mm orifice diameter. The CRDI engine results obtained were compared with the baseline date reported. The combustion chamber (CC) used for the study was toroidal re-entrant (TRCC). The experimental tests showed that BHO and BCO fuelled CRDI engine showed overall improved performance with 7 hole injector when engine was operated at optimized fuel IT of 10° before top dead centre (bTDC) and IP of 900 bar. The smoke emission reduced by 20% to 26% and NOx reduced by 16% to 20% in diesel and biodiesel powered CRDI engine as compared to conventional CI mode besides replacing diesel by biodiesel fuel (BDF).