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Six different ionic liquids based on dialkylimidazolium or quaternary ammonium cations associated with perfluorinated or bis(trifluoromethyl)sulfonyl amide anions were used as reaction media for ester synthesis catalyzed by both free Candida antarctica lipase B and α-chymotrypsin at 2% (v/v) water content and 50°C. All the assayed ionic liquids proved adequate media for enzyme-catalyzed transesterification, and in the case of lipase, the synthetic activity was clearly enhanced with respect to that obtained with organic solvents of similar polarity. In general, all the ionic liquids increased the thermal stability of both the enzymes. As for example, 1-ethyl-3-methylimidazolium tetrafluoroborate enhanced 5- and 4-times the synthetic activity and half-life time, respectively, of lipase in comparison to 1-butanol.