The use of capillary zone electrophoresis as an efficient method for the identification of urinary imidodipeptides of prolidase-deficient patients has already been reported. However, owing to the complexity of the components excreted, the resolution of electrophoretic patterns obtained was poor. Here we examine the use of micellar electrokinetic chromatography to enhance peak resolution in order to obtain better insight into the electropherograms of patients' urine. The usefulness of sodium dodecyl sulphate as surfactant is reported: refined electropherograms were achieved using 35 mM sodium borate, pH 8.3 containing 65 mM sodium dodecyl sulphate. Almost all peaks were baseline separated, collected and sequenced. This allowed us to define the exact imidodipeptide composition of patients' urine. The possibility of identifying and thus quantifying each single peak means that comparison of urinary imidodipeptide excretion patterns from different patients can be made and the hypothesis that peptide patterns can be correlated with differing clinical severity can be investigated.