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The on-line coupling of capillary electrophoresis (CE) with mass spectrometry using the electrospray-ionization mode (ESI-MS) is a promising combination of two analytical techniques. While CE provides high separation efficiency per unit of time, mass spectrometry affords high sensitivity and selectivity as well as molecular structural information. Three different projects are under way in our laboratory and are presented to illustrate the potential of CE-ESI-MS in pharmaceutical analysis. First, the determination of Ecstasy and other amphetamine derivatives in urine samples is reported. Second, the analysis of secondary metabolites, present in plant extracts such as tropane alkaloids, is depicted. Furthermore, the enantioselective analysis of pharmaceutical drugs and metabolites in human plasma is also described.