Aziridine derivatives are attracting pharmacological interest as protease inhibitors. Due to their two centers of chirality, the aziriclines studied here are mixtures of two diastereomers and corresponding enantiomers. Applying cycloclextrin-modified capillary electrophoresis resulted in a baseline separation of the four isomers. The most robust separation was obtained by means of 2 mm sulfated beta-cyclodextrin in 50 mm phosphate buffer of pH 2.5. Using this method, 0.25% of the trans-diastereomers aziridine could be precisely and accurately quantified in the presence of 99.75% of the cis-isomers. The corrected peak-area ratios, migration times, and resolutions were found to be robust with respect to small variations of voltage, buffer concentrations, pH, temperature, chiral selector concentration, and different lots.