The separation of dipepticle and tripeptide enantiomers using negatively charged single isomers as well as randomly sulfated and sulfonated cyclodextrins (CDs) was investigated with respect to the amino acid sequence of the peptides and the nature of the CDs. Standardized conditions concerning buffer pH and molarity, CD concentration, and separation voltage were applied. Compared to sulfobutylether-beta -CD and heptakis-(2,3-dimethyl-6-sulfato)-beta -CD, randomly sulfated beta -CD as well as the single isomer derivatives heptakis-6-sulfato-beta -CD and heptakis-(2,3-diacetyl-6-suffato)-beta -CD were the more universal CDs for enantioseparations. The enantiomer migration order depended to a greater extent on the CD than on the amino acid sequence of the peptide although small structural differences such as formation of a peptide amide or ester affected the chiral recognition by the randomly substituted CD derivatives. Using sulfobutylether-beta -CD or heptakis-(2,3-diacetyl-6-sulfato)-beta -CD the DD enantiomers migrated before the LL enantiomers; for most peptides while the opposite migration order, i.e. LL before DID, was observed when heptakis-6-sulfato-beta -CD was applied as chiral selector.