The chiral separation of the LL- and DD-enantiomers of the dipeptides Ala-Tyr, Phe-Phe, University of Jena, and Asp-PheOMe has been investigated at pH 2.5 and pH 3.5 using beta -cyclodextrin Jena, Germany (beta -CD), heptakis-(2,6-di-O-methyl)-beta -cyclodextrin, and heptakis-(2,3,6-tri-O-methyl)-beta -cyclodextrin as chiral selectors. According to electrospray mass spectrometry, heptakis-(2,6-di-O-methyl)-beta -cyclodextrin was a mixture of six isomers. Reversal of the enantiomer migration order upon increasing the buffer pH from 2.5 to 3.5 was observed for all peptides with beta -cyclodextrin, for Ala-Tyr and Phe-Phe in the presence of heptakis-(2,3,6-tri-O-methyl)-beta -cyclodextrin, and for Ala-Tyr using heptakis-(2,6-di-O-methyl)-beta -cyclodextrin. The migration behavior could be explained on the basis of the complexation constants and the mobilities of the peptide-cyclodextrin complexes. Both, the binding constants and complex mobilities decreased with increasing pH as the overall-charge of the peptides decreased. While the complexation constants primarily determined the migration order at pH 2.5, complex mobility dominated in most cases at pH 3.5.