The acyl glucuronide metabolites of endogenous as well as of xenobiotic compounds may undergo isomerization in vitro as well as in the human body. The parent acyl glucuronide and the isomerization products may react with endogenous protein to form products which in worst cases may act as antigens and thus create an allergic response. In the present paper new methods based on micellar electrokinetic or microemulsion electrokinetic chromatography for the separation of all isomerization products as well as the hydrolysis product of acyl glucuronides are described. In order to perform the separation at lower pH values in a reasonable time dynamically coated capillaries were used. This enables the electroosmotic flow to be high and constant even at low pH. The methods were developed using S-naproxen-beta-1-O-acyl glucuroride as the model substance. The assignment of the single peaks in the electropherogram was performed tentatively based on the sequential appearance of the isomerization products with time.