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In the post-genomic era, increasing our understanding of genotype-phenotypic correlation and its changes in diseases is of the highest priority in drug development. The phenotype of an organism consists of its physical/chemical attributes and its functional attributes. Metabolomics is a promising research tool for the phenotypic characterisation of an organism providing physical and functional assessment of a cellular metabolic network. Metabolomics has evolved from analytical biochemistry.With advances in nuclear magnetic resonance spectroscopy and mass spectrometry, metabolomics provides comprehensive analyses that detect and measure a wide range of small molecules (metabolites) in bodily fluid or tissue extracts. With automation, metabolomics analysis has the potential of a high throughput screening tool for measuring the effects of drugs in cells or in whole organisms, including humans. There are two major forms of metabolomics: metabolite profiling, which includes ‘fingerprinting’, and metabolic profiling, which includes tracer-based metabolomics. In this review, techniques and concepts for each of these modalities is reviewed. Examples of the applications of metabolomics in the characterisation of phenotype, determining the mode of action of compounds and detection of drug toxicity are presented.