The free fatty acid of crude karanja oil (Pongamia pinnata) was reduced and biodiesel was synthesized from pretreated oil under microwave irradiation. The process variables such as irradiation time, methanol-oil ratio and sulfuric acid concentration for pretreatment step; irradiation time, methanol-oil ratio and KOH concentration were optimized through the Box-Behnken experimental design. The free fatty acid of crude karanja oil was reduced to 1.11 +/- 0.07% with an optimal combination of 190 s irradiation time (180W), 33.83 (w/w)% methanol-oil ratio and 3.73 (w/w)% sulfuric acid concentration. An optimal combination of 150 s irradiation time, 33.4 (w/w)% methanol-oil ratio and 1.33 (w/w)% KOH concentration yielded 89.9 +/- 0.3% biodiesel. The model was validated by conducting experiments at optimal design conditions. The present work confirmed that the microwave energy has a significant effect on esterification and transesterification reaction. (C) 2010 Elsevier B.V. All rights reserved.