Molecularly imprinted microparticles imprinted against (S)-propranolol were synthesised and studied for use in capillary electrochromatographic separation of propranolol enantiomers. The imprinted microparticles were in the size range of 0.2–0.5 µm as determined by scanning electron microscopy. The microparticles were suspended, in high concentration, in the electrolyte and used to perform enantiomer separation by a partial filling technique.