Eight neutral cyclodextrins were tested for the enantiomeric separation of alanyl and leucyl dipeptides by capillary electrophoresis at pH 3, and seven out of the eight cyclodextrins proved suitable for the separation of one or more of the dipeptide enantiomer pairs. The best results were obtained with heptakis(2,6-di-O-methyl)-beta-cyclodextrin. The dipeptides that were separated were mainly the aromatic and the more lipophilic aliphatic dipeptides. Mobility difference plots at pH 3.0 with malonic acid-triethanolamine as background electrolyte showed that the aromatic dipeptides had higher affinities for the cyclodextrin than the nonpolar, aliphatic dipeptides. The results suggested that, under the conditions applied, the C-terminal amino acid rather than the N-terminal one is involved in the chiral discrimination.