A rapid, sensitive, and specific high-performance liquid chromatography (HPLC), diode-array detection, and mass-spectrometry techniques were developed for an identification of the constituents of Cortex Phellodendri and their metabolites in rat urine. The dose of 10 ml/kg of Cortex Phellodendri decoction was used for rats oral administration. 0 -24-h Urine was purified using a C18 solid-phase extraction cartridge, and then analyzed by an on-line MS detector. A total of 13 characteristic HPLC peaks were detected in the urine samples. Nine of them, including five alkaloids and four of their metabolites, were tentatively elucidated as magnoflorine (1), the glucuronide conjugate of demethyleneberberine (2), menisperine (3), jatrorrhizine 3-O-glucuronide (4), berberubine 9-O-glucuronide (5), jatrorrhizine (6), the monomethyl and monohydroxy catabolite of berberubine (7), palmatine (8), and berberine (9). Identification and structural elucidation of the metabolites were performed by comparing their MS n spectra data with those reported.