Electrokinetic supercharging, a powerful on-line preconcentration technique in CE, was for the first time hyphenated with ESI-MS for the on-line concentration and separation of five hypolipidaemic drugs. The electrophoretic separation was performed in a co-EOF mode using the EOF reversal agent, hexadimethrine bromide, in ammonium bicarbonate electrolyte, pH 9.00. The ionic strength and the amount of methanol in the buffer were optimised in a multivariate manner using artificial neural networks, with the optimal conditions being 60 mM ammonium bicarbonate containing 60% methanol, providing baseline resolution of the five hypolipidaemics within 20 min. Using electrokinetic supercharging, the sensitivity of the method was improved 1000-fold over a conventional injection under field-amplified sample stacking conditions with LODs of 180 ng/L. This is the first report of the separation of hypolipidaemics by CE. The developed method was validated and then applied to the determination of the target drugs in water samples from Hobart city.