Sertindole (1-[2-[4-[5-chloro-1-(4-fluorophenyl)-1H-indol-3-yl]-1-piperidinyl]ethyl ]-2-imidazolidinone), an atypical antipsychotic drug, was separated by capillary electrophoresis from its two main metabolites norsertindole and dehydrosertindole. The low solubility of the analytes in water (octanol-water partition coefficient is about 105) is overcome by the use of methanol (MeOH) and acetonitrile (ACN) as solvents for the background electrolyte (BGE). Mobilities were measured in BGEs with defined pH in a broad range. It was found that in MeOH the mobility of the analytes is mainly governed by acid-base equilibria, whereas in ACN other reactions like ion pairing and homoconjugation play a pronounced role and lead to a complex pattern of the mobility as function of the pH. However, separation can be obtained in less than 10 min in both solvent systems.