In this review, metabonomics, a combination of data-rich analytical chemical measurements and chemometrics for profiling metabolism in complex systems, is described and its applications are reviewed. Metabonomics is typically carried out using biofluids or tissue samples. The relevance of the technique is reviewed in relation to other '-omics', and it is shown how the methods can be applied to physiological evaluation, drug safety assessment, characterization of genetically modified animal models of disease, diagnosis of human disease, and drug therapy monitoring. The different types of analytical data, mainly from nuclear magnetic resonance spectroscopy and mass spectrometry, are summarized. The outputs from a metabonomics study allow sample classification, for example according to phenotype, drug safety or disease diagnosis, and interpretation of the reasons for classification yields information on combination biomarkers of effect. Transcriptomic and metabonomic data is currently being further integrated into a holistic understanding of systems biology. An assessment of the possible future role and impact of metabonomics is presented.