Abstract: Gas chromatography/Time-of-Flight mass spectrometry (GC/TOF-MS) based metabonomic studies were undertaken to investigate the in vivo metabolic variations caused by metronidazole treatment in hyperlipidemia hamster.Terminal restriction fragment length polymorphism (T-RFLP) was used to investigate the composition of gut microbiota of hamster.Obvious metabolic and gut microbiota disorders were observed in the model hamsters.After treatment with metronidazole,the lipid metabolism was regulated towards normal level.Moreover,the intragastric administration of metronidazole reversed part of gut microbiota disturbed by high fat diet.However,oral-administered metronidazole can also perturb other metabolites as well as normal gut flora of hamster.The results remind us that the perturbation of metabolism should be paid attention to before the application of metronidazole as a hypolipidemic agent.