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Metabonomics defines as "the study of multivariate metabolic responses of complex organisms to physiological and/or pathological stressors, including the consequent disruption of systems regulation".1;2 Technically, metabonomics investigations usually consist of the collection of metabolic profiles using NMR spectroscopy or MS spectrometry and analysis of the collected data using appropriate multivariate statistical techniques.1H NMR spectroscopy has been used widely due to its capability of simultaneously detecting a wide range of small molecule metabolites, thus providing a "snapshot of the metabolite composition" of blood, other biofluids and tissues.3;4 Metabonomics has been proven extremely powerful analytical tool and hence found successful applications in many research areas including molecular toxicology, pathology, physiology, functional genomics and environmental sciences.As a holistic approach to solve biological problems, metabonomics has become an important part of global systems biology.In this presentation, examples of metabonomics application in studying disease etiology, such as diabetes, gastro intestinal disease5;6 and parasitic diseases7;8 will be given and the role of gut microbiota will be discussed.