ABSTRACTBiodiesel (fatty acid methyl or ethyl esters), a clean alternative fuel, has attracted considerable attention as it is a renewable, biodegradable and non-toxic fuel and can generally be used as a substitute for diesel. The present study, biodiesel production from jatropha oil and karanja oil was studied with immobilized Rhizopus oryzae MTCC (262) cells. Prior to the optimization experiments, single point optimization studies were conducted to select the alkyl source (methanol), organic solvent (n-hexane), optimum solvent quantity (20% w/w of oil) and bead size (0.24 cm) using R. oryzae cells. Effect of reaction time (42 h) and optimum agitation speed (150 rpm) on percentage biodiesel yield were studied. Response surface optimization experiments were carried out for optimizing the operating conditions namely reaction temperature, reaction time, added water content, catalyst concentration and molar ratio of alcohol to oil. Maximum biodiesel yields of 80.5% and 78.3% for jatropha oil and karanja oil.