In this review we summarize some aspects of the enantiopreference of the lipase from Candida rugosa following structural analysis of complexes of this lipase with two enantiomers of an analog of a tetrahedral intermediate in the hydrolysis of simple esters. The analysis of the molecular basis of the enantiomeric differentiation suggests that these results can be generalized to a large class of lipases and esterases. We also summarize our experiments on identification of the key regions in the lipases from Geotrichum candidum lipase responsible for differentiation between fatty acyl chains.