A new analytical method for enantioselective separation of DL-amino acids derivatized by N-fluorenylmethoxycarbonyl-L-alanyl N-carboxyanhydride (FMOC-L-Ala-NCA) using capillary electrophoresis was developed. Separation parameters, such as composition and pH of the background electrolyte, and concentration of gamma-cyclodextrin (in capillary zone electrophoresis) and sodium dodecyl sulfate (in micellar electrokinetic chromatography) were optimized. The separation method was validated and it suits well for purity analysis. Detection limit of the method was 0.2% of the minor enantiomer in the major one. The level of racemization in coupling during solid-phase peptide synthesis was studied using capillary electrophoresis with gamma-cyclodextrin as a chiral selector. The anchorage of the first (C-terminal) amino acid derivative to the solid supports bearing the hydroxylic groups is the key step of the synthesis affecting the extent of its racemization. FMOC-L-phenylalanine was chosen as the suitable model amino acid derivative making it possible to study the degree of racemization of N-fluorenylmethoxycarbonyl-L-alanine-L-phenylalanine synthesized on different polymer resins, using the different condensation agents.