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Capillary electrophoresis (CE) has emerged as a powerful technique for comprehensive physicochemical characterization of monoclonal antibodies (mAbs) as well as other therapeutic modalities. The method provides high resolution separation and high sensitivity characterization for analysis of therapeutic biomolecules. CE based techniques such as sodium dodecyl sulphate capillary gel electrophoresis (SDSCGE, also referred to as CE SDS), capillary zone electrophoresis (CZE) and imaged capillary isoelectric focusing (iCIEF) have been increasingly adopted to assess size heterogeneity, glycosylation heterogeneity and charge heterogeneity in mAbs and related therapeutic modalities. This paper reviews the latest application developments of CE based methods for routine release testing, stability testing and in-depth characterization. In addition, advantages and disadvantages of each of these techniques are critically discussed.