In this study, we have investigated the ultrasound assisted acid catalyzed transesterification of Jatropha oil. A statistical experimental design (Box-Behnken) is coupled to simulations of cavitation bubble dynamics. Acid catalyzed esterification was rather insensitive to ultrasound irradiation, while the beneficial effect of sonication on transesterification reaction was only through the intense micro-mixing induced by ultrasound. Transient cavitation in methanol did not render any impressive effect. The transesterification system was revealed to be strongly controlled by intrinsic kinetics and mass transfer resistance. The optimum values of experimental variables have been determined as: alcohol to oil molar ratio approximate to 7, catalyst concentration approximate to 6% w/w oil and temperature approximate to 70 degrees C. The influence of these variables is highly involved and interlinked, and any deviation from its optimum value leads to sharp reduction in the FAME yield. Results of this study illustrate that sonication does not change the chemistry of acid-catalyzed transesterification and the beneficial effect is only of physical nature, which is further limited by the intrinsic kinetics and mass transfer. (C) 2013 Elsevier B.V. All rights reserved.