Capillary electrophoresis (CE) is a versatile analytical method used to characterize glycoproteins. We have used several modes of CE separation such as CE-SDS gel, imaged capillary isoelectric focusing (icIEF), and capillary zone electrophoresis (CZE) to study therapeutic glycoprotein products. CE-SDS gel is applied to characterize the glycan occupancy and number of glycosylation sites, and icIEF is used to study the charge heterogeneities due to sialic acids in glycoproteins. To further characterize the glycoprotein, removal of N-linked glycans is necessary and a CZE technique is employed to analyze each glycan moiety. Examples from a monoclonal antibody, erythropoietin, and granulocyte colony-stimulating factor are presented here to demonstrate the utility of these CE modes. The details of sample preparation and separation conditions for each CE mode are described in this chapter.