Abstract A method for purification of cis-9,trans-11 isomer of conjugated linoleic acid (CLA) is described. Lipase from Candida cylindracea (CCL) was highly selective towards cis-9,trans-11 isomer and was chosen to catalyze esterification of a mixture of two CLA isomers. The effect of various parameters on the esterification process of an almost equimolar mixture of cis-9,trans-11 (44.0%), trans-10,cis-12 (42.5%) and other CLA isomers (13.5%) was studied. The influence of alcohol substrate, CLA/alcohol molar ratio, lipase amount, reaction temperature, pH and time of the reaction on the total esterification and cis-9,trans-11 isomer purity in ester fraction were examined. The highest isomeric excess of cis-9,trans-11 isomer on trans-10,cis-12 CLA and good esterification degree was observed when the esterification condition were as follows: CLA/2-propanol molar ratio, 1:5; water, 200% wt of CLA; CCL, 24 μg of CCL/mg CLA; temperature 30 C; time of reaction 6 h and when mixture enriched in cis-9,trans-11 CLA was used as a substrate for esterification. A preparative scale purification combining crystallization and one step enzymatic process were made to afford purified cis-9,trans-11 (94.2%) with total recovery of 31%.