SummaryAmino acids are cations at low pH and can be readily separated by capillary electrophoresis provided an alkanesulfonic acid is added to the electrolyte carrier. Formation of a positive net charge on the bare fused-silica surface at low pH was confirmed by measurement of an anodic electroosmotic flow. The addition of ethanesulfonic acid or octanesulfonic acid to the electrolyte carrier causes a reversal of the EOF. A mechanism is proposed in which the alkanesulfonic acid adsorbs to the positively-charged capillary wall through electrostatic attraction. Adsorption of a second molecule of alkanesulfonate by hydrophobic attraction to the carbon chain forms a negatively-charged coating on the capillary wall. The alkanesulfonate also imparts selectivity to the system by participation in ionpairing interactions with the native amino acids to improve resolution. The CE separation of a mixture of the twenty common amino acids at pH 2.8 with direct absorbance detection at 185 nm resulted in 17 amino acid peaks in 20 minutes with a 30 kV applied voltage. The effect of several variables was studied including electrolyte carriers containing different alkanesulfonic acids, the influence of pH, applied voltage, and concentration of electrolyte carrier.