BackgroundSenkyunolide I (SEI) is one of the most important bioactive phthalides of Ligusticum chuanxiong Hort. (Umbelliferae), a Traditional Chinese Medicine. Our previous studies suggested that it might be developed as a potential treatment for migraine.MethodsIn this paper, we aimed to isolate and characterize the main metabolites of SEI after gavage feeding in rats. Their structures were identified precisely on the basis of nuclear magnetic resonance (NMR) spectroscopy and UPLC/Q-TOF-MS spectrometry. We also established the main metabolic pathways of SEI in rats.ResultsFour metabolites (M1-M4) were isolated, for the first time, from bile samples of rats by preparative high-performance liquid chromatography. Their structures were determined as SEI-6S-O-β-D-glucuronide (M1), SEI-7S-O-β-D-glucuronide (M2), SEI-7S-S-glutathione (M3) and SEI-7R-S-glutathione (M4) on the basis of the molecular mass of the analytes, using ultra performance liquid chromatography/quadrupole-time-of-flight mass spectrometry and 1D and 2D NMR.ConclusionsThe results demonstrated that glucuronide and glutathione conjugation were the major pathways of SEI metabolism in vivo, and the configuration at the 7th-position could be inverted during glutathione conjugation.