Metabolomics is the unbiased identification and state-specific quantification of all metabolites in a cell, tissue or whole organism, and has developed rapidly into one of the cornerstones of postgenomic techniques for the quantitative analysis of molecular phenotypes. These large-scale analyses of metabolites are intimately bound to advancements in MS technologies and have emerged in parallel with the development of novel mass analyzers and hyphenated techniques, as well as with the combination of different techniques to cope with the physicochemical diversity of a metabolome. This review gives a brief description of the development and applications of these technologies in biochemistry and systems biology, and discusses their significance in the postgenomic era. Especially, the systematic relation between high-throughput metabolomic data and their interpretation with respect to the underlying biochemical regulatory network is discussed.