Capillary electrophoresis (CE) with end-column electrochemical detection (EC) of barbituric acid (BA) and 2-thiobarbituric acid (TA) has been described. Under optimum condition, BA and TA were separated satisfactorily, and a response of high sensitivity and stability was obtained at a detection potential of 1.25 V versus Ag/AgCl. Optimized end-column detection provides detection limit as low as 0.5 and 0.1 muM for BA and TA, respectively. The calibration graph was linear over three orders of magnitude. The relative standard deviations (n=10) of peak currents and migration times obtained for both BA and TA were 3.4, 3.7, and 1.7, 1.2%, respectively. The proposed method has been applied to analyze water sample with satisfactory results.