Corynoline is a 1,3-benzodioxole-containing isoquinoline alkaloid isolated from Corydalis bugeana Turcz., a traditional herbal medicine. Corynoline has reportedly demonstrated multiple pharmacologic properties. Previous studies have also shown that corynoline induced cytotoxicity and inhibited cytochrome P450 (CYP) enzymes, but the mechanisms of the adverse effects remain unknown. The major objective of the present study was to identify reactive metabolites of corynoline responsible for the cytotoxicity and enzyme inhibition. Three oxidative metabolites (M1-M3) were detected by liquid chromatography-tandem mass spectrometry in rat liver microsomal incubations after exposure to corynoline. M1 and M2 were two isomers of catechol derivatives, and M3 was a dicatechol. The M1-M3 metabolites were also observed in urine of rats given corynoline. A total of four N-acetylcysteine (NAC) conjugates (M4-M7) were detected in microsomes containing corynoline, NAC, and NADPH. Apparently, M4 and M5 were derived from M1, M6 resulted from M2, and M7 was a M3-derived NAC conjugate. This indicates that corynoline was bioactivated to ortho-quinone derivatives. No corynoline-derived NAC conjugates (M4-M7) were detected in urine of rats given corynoline; however, three corresponding cysteinylglycine conjugates (M8-M10) were observed instead. Recombinant P450 enzyme incubations demonstrated that the CYPs 2C9, 3A4, and 2C19 were mainly involved in metabolic activation of corynoline. The metabolism study facilitates the understanding of corynoline-induced cytotoxicity and P450 enzyme inhibition.