Metabonomics is the branch of science concerned with the quantitative understandings of the metabolite complement of integrated living systems and its dynamic responses to the changes of both endogenous factors (such as physiology and development) and exogenous factors (such as environmental factors and xenobiotics). As a holistic approach, metabonomics detects, quantifies and catalogues the time related metabolic processes of an integrated biological system, ultimately, relates such processes to the trajectories of the pathophysiological events. Ever since its birth in 1999, metabonomics has already been described in more than 800 scientific papers and half dozen patents, amongst which almost 700 papers were experimental articles. Now, metabonomics has been established as an extremely powerful analytical tool and hence found successful applications in many research areas including molecular pathology and physiology, drug efficacy and toxicity, gene modifications and functional genomics, and environmental sciences. This holistic approach has thus become an important part of systems biology and has now evolved to be a unique part in global systems biology. The essence of metabonomics and some of the present applications were reviewed to illustrate the rapid development of this extremely exciting new frontier.