Peptides represent a large and complex group of biologically active substances. Their occurrence and function in nature are very variable and of vital importance. Peptides act for example, as hormones, neurotransmitters, immunomodulators, coenzymes or enzyme inhibitors, drugs, toxins, and antibiotics. The demands of chemists, biochemists, and all other specialists dealing with peptide research and applications for the methods that should be able to separate and characterize peptide preparations both qualitatively and quantitatively are continuously increasing. Consequently, the application of capillary and free-flow zone electrophoresis for peptide analysis, preparation, and physicochemical characterization is an area of great importance.