Microemulsion electrokinetic chromatography (MEEKC) in a suppressed electroosmotic flow environment has been evaluated for the separation of compounds of pharmaceutical interest. The separation medium was 0.8% (w/w) n-octane, 6.0% (w/w) sodium lauryl sulphate (SDS), 6.6% (w/w) 1-butanol, 20.0% (w/w) 2-propanol, and 66.6% (w/w) 25 mM phosphate buffer pH 2.5. The electroosmotic flow was effectively suppressed by use of this acidic microemulsion. The separation voltage was reversed, with the anode placed at the capillary outlet, and the negatively charged microdroplets of n-octane migrated towards the detector. Several steroids, benzodiazepines, antidepressants, antipsychotic drugs, and antiepileptic drugs were effectively separated on the basis of their different interactions with the migrating microdroplets of n-octane. The MEEKC system was briefly validated for the determination of the antidepressant citalopram in commercial tablets; quantitative data were in accordance with the label claim (5.5% deviation) and intra-day and inter-day variation were 1.63% RSD and 3.54% RSD, respectively.