This chapter describes the basic principles of protein analysis by capillary electrophoresis, and provides an overview of the literature and thus a comprehensive summary of special topics in this field. The “Materials and Methods” section includes the main experimental points to be taken into consideration, namely, sample pretreatment, reduction of protein adsorption to capillary wall, increase of selectivity, detection modes, and special electrophoretic modes. Because there are many capillary electrophoretic methods for protein analysis, not all experimental steps are listed; however, the main references are cited. Additional experimental information can be found in the Notes. Finally, an overview of the most relevant applications , divided according to the origin of the samples into human proteins, food and agricultural products, pharmaceutical proteins, proteome, and special proteins, is given with the relevant literature.