A capillary electrophoretic method has been established for the separation of the enantiomers of clenbuterol. The effects of pH value, composition of the background electrolyte, concentration of carboxymethyl-β-cyclodextrin (CM-β-CD), capillary temperature and running voltage have been investigated. The two enantiomers were separated in an uncoated capillary with phosphate buffer (50 mmol/L, pH 3.5) containing 10 mmol/L CM-β-CD. The capillary temperature was at 15°C and applied voltage was at 20 kV. The inclusion complex of CM-β-CD and clenbuterol was synthesized and characterized by two-dimensional rotating frame spectroscopy (2D ROESY). Based on the 2D ROESY analysis, an inclusion structure of the clenbuterol/CM-β-CD complex was proposed, in which clenbuterol penetrated CM-β-CD in a tilted manner due to the interaction of intermolecular hydrogen bonds between clenbuterol and CM-β-CD.