The determination of quaternary ammonium ions by capillary electrophoresis (CE) is reviewed. The analytes include tetraalkylammonium and alkylbenzyldimethylammonium compounds frequently used as antiseptic and antibacterial agents as well as in various household products, several plant growth regulators and herbicides, by-products in bile acid sequestrants, and a range of anticholinergic drugs. Besides direct and indirect UV detection, hyphenation with electrospray mass spectrometry is particularly suited for quaternary ammonium ions and may lower the detection limits by two orders of magnitude. In comparison with established liquid chromatographic techniques, CE may exhibits superior separation efficiency. Applications in routine analysis have demonstrated that CE is reliable and robust enough to represent a real alternative to chromatography.