A rapid, sensitive method for the determination of morphine and amphetamine was developed using capillary zone electrophoresis coupled with electrospray interface (ESI), ion-trap tandem mass spectrometry (CE-ESI-MS2). Morphine and amphetamine were separated in 20 mM ammonium acetate buffer (pH 6.6) and detected by ion-trap mass detector in different analytical time segments (0-6.25 min for amphetamine and 6.25-12.0 min for morphine) in which the tune file for each compound was used separately. Molecular ions of morphine (m/z 286) and amphetamine (m/z 136) were detected at 5.77 and 6.83 min, respectively, while product ions of MS2 for each compound (m/z 229, 201 for morphine and m/z 119 for amphetamine) were detected almost exactly at the same time with their parent compounds. The limits of detection (LOD) for MS2 determination were 30 and 50 ng/mL for amphetamine and morphine, respectively, with an S/N ratio of 3. For more sensitive detection of morphine, the sample was injected for a longer time (i.e., 80 s) and hydrodynamically transported into a CE capillary for MS detection. Morphine and its product ion appear at 0.36 and 0.39 min on the ion chromatogram, respectively, with a five-fold increase of detection sensitivity (LOD, 10 ng/mL). The CE-MS system thus established was further applied for forensic urine samples screened as morphine-positive by fluorescence polarization immunoassay (FPIA). These results indicated the feasibility of CE-ESI-MS2 for confirmative testing of morphine in urine sample.