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Ethnopharmacological relevance: Xiaoyaosan (XYS) is a famous traditional Chinese medicine prescription with a long history use in the clinic.It contains eight herbs: Bupleurum chinense DC., Paeonia lactiflora Pall., Poria cocos (Schw.) Wolf, Angelica sinensis (Oliv.) Diels, Zingiber officinale Rosc., Atractylodes macrocephala Koidz., Glycyrrhiza uralensis Fisch., and Mentha haplocalyx Briq.The aim of this study is to establish the metabolic profile of major depressive disorder(MDD) and investigate the action mechanism of the aqueous extract of XYS effect using a metaboiomics approach.Material and methods: 21 patients with MDD were recruited from the traditional Chinese medicine department of the First Affiliated Hospital at Shanxi Medical University, the patients were treated with aqueous extract of XYS for eight weeks and urine samples were collected every two weeks.Contents of small molecular endogenous metabolites in urine samples were measured by nuclear magnetic resonance and analyzed by multivariate statistical methods.Results: After XYS intervention for six weeks, the Hamilton depression rating scale(HDRS) scores was significantly decreased compared to baseline (p < 0.01), depressive symptom have been significantly eased up according to HDRS scores.Totally 11 metabolites have been found significantly changed during XYS treatment.Trimethylamine N-oxide, citrate, phenylacetyglycine, tyrosine, m-hydroxyphenylacetate, malonate, creatine, hippurate and dimethylamine increased significantly (p < 0.05, p < 0.01), while the levels ofsuccinate and nicotinate decreased significantly (p < 0.05, p < 0.01) after XYS intervention of eight weeks compared with the M DD before treatment.These significant perturbations are involved in amino acid metabolism, energy metabolism and bacterial metabolism, XYS produced an obvious antidepressant effect.The results demonstrated that urine metabonomics was a powerful tool in clinical diagnosis and treatment of MDD for providing information on changes in metabolites.Conclusion: These findings demonstrated that XYS produced a great antidepressant effect for the treatment of MDD cases and the mechanism of action involves amino acid metabolism, energy metabolism and bacterial metabolism.metabonomic approaches could be powerful tools for the investigation of the biochemical changes in pathological conditions or drug treatment.