The presence of two of the metabolites of heroin, free morphine and morphine 3-beta-D-glucuronide (MO3G) in acidified urine samples was simultaneously determined by capillary zone electrophoresis (CZE). In a run buffer containing 50 mM sodium borate and 250 mM boric acid (pH 8.6), free morphine migrates before a group of neutral compounds (peak N) in urine, which move with the velocity of electro-osmotic flow. In contrast, the glucuronidated form is negatively charged and migrates behind peak N. Both analytes can be precisely identified within their respective analytical window by their migration time with respect to peak N. The on-line multi-wavelengths scanning of the peak permits further confirmation. The detection sensitivity of both analytes was increased three-four fold if the samples were introduced with electro-injection as compared with hydrodynamic injection. Limits of detection (LOD) of free and conjugated morphine using electro-injection were 200 ng/mL and 500 ng/mL, respectively, determined at a 3:1 signal to noise ratio. A dramatic increase of free morphine was observed after acid hydrolysis of the urine concomitantly with the decrease of the glucuronidated form. We conclude that CZE is a rapid, simple, sensitive and useful screening technique for detection of heroin metabolites in the urine.