The chiral separation of several dipeptide enantiomers, derivatized by naphthalene-2,3-dialdehyde (NDA), was achieved by use of cyclodextrin-modified micellar electrokinetic chromatography (CD-MEKC), The dipeptides contained one or two chiral centers, In the case of several dipeptides containing two chiral centers, all four of the optical isomers could be separated and baseline resolved in less than 15 min with 20 mM gamma-CD and 50 mM sodium dodecyl sulphate (SDS) in the background electrolyte. The order of elution of these derivatized dipeptides was explained by considering important chemical equilibria in the SDS, CD and peptide system, Additionally, the influence of geometric location of the chiral center, the structure of the side-chain and the effect of CD concentration on the resolution are discussed.