The adverse influence of chloride impurities on the lipase-catalyzed transesterification in ionic liquid is described. The activity of lipase from Rhizomucor miehei exponentially decreased with increasing Cl- content in 1-octyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]amide, [Omim][Tf2N], and the activity of lipase in [Omim][Tf2N] mixture containing 2% [Omim][Cl] was only about 2% of the activity in pure [Omim][Tf2N]. The activity of lipase from Candidantarctica linearly decreased at about 5% with every 1% increase in [Omim][Cl] with there being no activity in [Omim][Tf2N] containing about 20% [Omim][Cl].