Liquid chromatography/electrospray ionization tandem mass spectrometry (LC/MSn) was used to identify trace levels of in vivo metabolites after the administration of isovalertatin M23 or isovalertatin D23 to rats. The biosamples of urine, feces, and ileum incubation were pre-treated by solid-phase extraction (SPE), and then chromatographed with a reversed-phase C8 column with acetonitrile/1.5 mM aqueous ammonia (18:82, v/v) as the mobile solvent. The parent drug and the possible metabolites were identified by two independent qualitative parameters, retention time and collision-induced dissociation product ions. Nine and seven metabolites were successfully characterized from biosamples after administration of isovalertatins M23 and D23, respectively, to rats. The metabolism seemed to take place in the rat intestinal tract, and metabolic pathways were identified including isovaleryl de-esterification and hydrolysis of α-glucose units located either at the reducing or the non-reducing terminus. Copyright © 2006 John Wiley & Sons, Ltd.