The potential of nonaqueous capillary electrophoresis was investigated for the simultaneous separation of fluoxetine hydrochloride, its meta-isomer, and other related compounds. The resolution of these compounds was compared in aqueous and nonaqueous media. Baseline separation of the studied solutes required a buffer electrolyte solution composed of 25 mm ammonium acetate and 1 m acetic acid in acetonitrile, an applied voltage of 30 kV and a temperature of 20degreesC. Selectivity was considerably affected by the nature of the solvent (water, methanol, and acetonitrile). Moreover, substituting acetate by formate, in the background electrolyte resulted in migration time changes, which were attributed to an ion-pairing phenomenon. Finally, the method was successfully coupled on-line with electrospray ionization-mass spectrometry (ESI-MS) and allowed significant selectivity and sensitivity enhancement. The effect of ESI-MS parameters, such as nebulizing gas pressure, sheath liquid composition and flow rate, on resolution and method sensitivity was also discussed.