Fatty acids methyl esters (FAME) have been prepared under microwave irradiation, using homogeneous catalysis, either in batch or in a flow system. The quality of the biodiesel obtained has been confirmed by GC analysis of the isolated product. While the initial experiments have been performed in a small scale laboratory batch reactor, the best experiment has been straightforward converted into a stop-flow process, by the use of a microwave flow system. Compared with conventional heating methods, the process using microwaves irradiation proved to be a faster method for alcoholysis of triglycerides with methanol, leading to high yields of FAME. (c) 2006 Elsevier Ltd. All rights reserved.