Allantoin, uric acid (UA), hypoxanthine (Hx) and xanthine (X) were determined on carotid plaque by capillary zone electrophoresis (CZE) and high-performance liquid chromatography (HPLC). Comparison of the results showed that capillary zone electrophoresis may have similar or even superior analytical performance to HPLC, especially for the determination of allantoin in biological samples.