The purpose of this study was to develop an analytical method to quantify the relative activities of carboxylesterases (CESs) in biological samples. Taking the advantage of loperamide, a specific carboxylesterase 2 (CES2) inhibitor, and bis-p-nitrophenyl phosphate (BNPP), an irreversible CESs inhibitor, we propose for the first time a capillary electrophoresis (CE) method that enables detecting and distinguishing CES2 activity from other CESs in complex biological samples. The capillary electrophoresis method proved to be fast, simple, repeatable, and applicable to the measurement of the specific activity of CESs. The method was successfully applied to the evaluation of human cells overexpressing human carboxylesterase 2 (hCE-2) and to several mammalian sera, using extremely small amounts of samples in comparison with traditional spectrophotometric methods. The same rationale can be applied to establish methods for determining the activity of other isoenzymes, using the appropriate specific inhibitors.