In the present study, 10 different ionic liquids based on 1-alkyl-3-methylimidazolium and 1-alkyl-3-methyl pyridinium cations combined with hexafluorophosphate, bis{(trifluoromethyl)sulfonyl}imide, tetrafluoroborate and trifluoromethanesulfonate were tested as reaction media for the transesterification of sunflower or waste cooking oils and 1-methanol catalyzed by an immobilized Candida antarctica lipase B (Novozyme 435). The reaction was also carried out in isopropanol and methyl tert-butyl ether as reference solvents. The ionic liquids 3-octyl-1-methylimidazolium hexafluorophosphate and 3-octyl-1-methylimidazolium bis{(trifluoromethyl)sulfonyl}imide permitted higher fatty acid methyl esters conversions than obtained with reference solvents. When the effect of cation and anion composition of the ionic liquid on the synthetic activity of C. antarctica lipase B (CaLB) was analysed, the activity was enhanced by increasing cation hydrophobicity and decreasing anion nucleophilicity. The optimal water content and methanol to oil substrate molar ratio were also determined, using the ionic liquid 3-octyl-1-methylimidazolium hexafluorophosphate as reaction media, and were found to be 1% and 12:1, respectively. The transesterification reaction was also carried out using waste cooking oils as feedstock and fatty acid methyl esters production was similar to that obtained with sunflower oil. (C) 2011 Elsevier Ltd. All rights reserved.