In the present work, synthetic cyclohexa- and cycloheptapeptides previously singled out by a combinatorial chemistry approach have been evaluated as chiral selectors in capillary electrophoresis. By applying the countercurrent migration technique and employing a new adsorbed coating, a series of dinitrophenyl amino acids as well as some chiral compounds of pharmaceutical interest have been evaluated for enantio-recognition. The results thus obtained led to a deeper investigation of the chiral discrimination process, by carrying out nuclear magnetic resonance (NMR) studies on selected cyclopeptide-analyte complexes. These studies shed light on the chemical groups involved in the analyte-selector interaction and provided useful information for a wider application of these cyclopeptides in the separation of other drug enantiomers.