The effect of microwave heating and ultrasound on the purity of the methyl ester phase was studied. During the transesterifications process triglyceride esters were turned into methyl esters (FAME), e.g., methanol replaces the glycerol: The process of FAME formation was complicated and went through the formation of diglycerides and monoglycerides, which were the by-products that reduce selectivity and increase the separation time. Glycerol produced as the heavier phase sinked to the bottom and biodiesel as the lighter phase floated on top and can be separated. Microwave heating did not give a considerable positive effect for transesterifications reactions with low catalyst concentration, however, ultrasound heating showed positive effect. At > 40°C, ultrasound transesterification ran better than the reaction with convection heating and yielded product of higher purity even low catalyst concentration was used. This is an abstract of a paper presented at the 18th International Congress of Chemical and Process Engineering (Prague, Czech Republic 8/24-28/2008).