In this study we tried to develop, test and optimize a batch microwave system using waste cooking vegetable oil (WCVO) that was used as biodiesel feedstock. Two catalysts, sodium hydroxide (NaOH) and potassium hydroxide (KOH) were tested in this study. Transesterification reactions between oil and methanol were carried out in presence of microwaves. It was observed that by using of microwaves, the reaction times were drastically reduced. As high as 99.5% conversions could be achieved for 0.5% KOH concentration. Moreover, quality analysis of biodiesels according to international standards was performed and the samples were found to meet the necessary specifications.