Metabolomics is a systems approach to studying the small, endogenous metabolites in an organ, biofluid or whole organism. It can be used as a screening tool for metabolite profiling, or to detect changes in the metabolome brought on by external or internal stressors. The purpose of this review is to summarize and evaluate the information obtained from the application of metabolomics in fish research and to discuss its future potential. It is already clear that metabolomics has contributed new knowledge about fish in areas such as basic physiology and development, disease, water pollution and aspects concerning fish as foodstuffs.