The present study investigated the separation of bicyclic β-amino acids with bicyclo[2.2.2]octane, bicyclo[3.1.1]heptane and cyclopenta[d][1,2]oxazole core structures by capillary electrophoresis using native cyclodextrins as well as neutral and charged derivatives as chiral selectors. The amino acids were derivatized with dansyl chloride to provide a UV chromophore. Separations were carried out at 20°C in a 48.5/40cm, 50µm fused-silica capillary at an applied voltage of 20kV. Fifty millimolar sodium phosphate background electrolytes pH2.5 and 7.2 containing either 5 or 30mg/mL of the CDs were used. For the majority of the investigated CDs, enantioseparations could only be achieved at pH 2.5 when the analytes are positively charged. Successful enantioseparations as negatively charged analytes at pH7.2 were only observed for few compounds. In the case of methyl-γ-cyclodextrin, opposite enantiomer migration order was observed in pH2.5 or 7.2 background electrolytes. Dependence of the enantiomer migration order on the size of the cavity of the cyclodextrins was also found. Furthermore, the degree of methylation of β-cyclodextrin derivatives affected the migration order of several analyte enantiomers.