A previously developed capillary electrophoresis method for the simultaneous separation and enantioseparation of thalidomide (TD) and its hydroxylated metabolites was extended to one additional biotransformation product. The dual chiral selector system using native beta-cyclodextrin (beta-CD) and the negatively charged sulfobutyl ether-beta-CD (SBE-beta-CD) was slightly modified up to a concentration of 12 mg/mL running buffer of each CD. The carrier mode in which these buffer additives transport the neutral compounds to the detector as well as the use of a polyacrylamide-coated capillary were necessary to achieve reproducible enantioseparations of all eight analytes. The optimized method was applied to the analysis of the in vitro biotransformation of TD by rat liver microsomes. The S-enantiomer undergoes metabolism preferentially by hydroxylation in the phthalimide ring, whereas R-(+)-TD is mainly transformed to diastereomeric 5'-hydroxythalidomide (5'-OH-TD) pairs. The chiral capillary electrophoresis of incubation samples of TD enantiomers in combination with X-ray diffraction data allowed us to determine the absolute configuration of all metabolites and furthermore to follow the enantio-and stereoselective effects of metabolism in detail.