BACKGROUND: Biodiesel is increasingly perceived as an important component of solutions to the important current issues of fossil fuel shortages and environmental pollution. Biocatalysis of soybean oils using soluble lipase offers an alternative approach to lipase-catalyzed biodiesel production using immobilized enzyme or whole-cell catalysis. The central composite design (CCD) of response surface methodology (RSM) was used here to evaluate the effects of enzyme concentration, temperature, molar ratio of methanol to oil and stirring rate on the yield of fatty methyl ester. RESULTS: Lipase NS81006 from a genetically modified Aspergillus oryzae was utilized as the catalyst for the transesterification of soybean oil for biodiesel production. The experimental data showed that enzyme concentration, molar ratio of methanol to oil and stirring rate had the most significant impact on the yield of fatty methyl ester; a quadratic polynomial equation was obtained for methyl ester yield by multiple regression analysis. The predicted biodiesel yield was 0.928 (w/w) under the optimal conditions and the subsequent verification experiments with biodiesel yield of 0.936 +/- 0.014 (w/w) confirmed the validity of the predicted model. CONCLUSION: RSM and CCD were suitable techniques to optimize the transesterification of soybean oil for biodiesel production by soluble lipase NS81006. The related lipase NS81006 reuse stability, chemical or genetic modification, and transesterification mechanism should be taken into consideration. (c) 2007 Society of Chemical Industry.