Meisoindigo has been effectively applied for the treatment of chronic myelogenous leukemia (CML). Although the metabolic profile of meisoindigo has been studied in liver, information relevant to extrahepatic metabolism of meisoindigo is absent in kidney so far. In this study, the metabolism of meisoindigo in rat kidney microsomes was qualitatively and quantitatively investigated by liquid chromatography/tandem mass spectrometry (LC/MS/MS), in terms of metabolite identification, metabolic stability, metabolite formation and gender effect. The metabolic profiling was accomplished by integration of multiple reaction monitoring (MRM) with conventional full MS scan followed by MS/MS methodology. The major in vitro metabolites of meisoindigo in rat kidney microsomes were identified as stereoselective 3,3' double-bond reduced meisoindigo, whereas the minor metabolites were regioselective phenyl monohydroxylmeisoindigo. An LC/MS/MS method for quantification of meisoindigo in rat kidney microsomes was also developed and validated. The calculated in vitro half-life (t(1/2)) values of meisoindigo in male and female rat kidney microsomes were 107.8 +/- 17.0 min and 130.0 +/- 12.9 min, respectively. There were no statistically significant differences between different genders in the metabolic stability profiles of meisoindigo. The reductive metabolite-formation profiles of meisoindigo in male and female rat kidney microsomes were plotted semi-quantitatively as well. The information regarding in vitro renal metabolism of meisoindigo provided a better understanding of the role of the kidney in the disposition of meisoindigo.