Metabonomics is a new member in the omics field following the development of genomics, transcriptomics and proteomics, with its research object being the collection of metabolites-metabolome, the downstream products of life. Even with the development of past decade, there are still many problems to be solved in the area of experimental techniques, data analysis and results annotation. Any xenobiotics would cause the disturbance of homeostasis of organisms, resulting in the changes of metabolites. Consequently, toxicology is one of the major application areas of metabolomics, and is the earliest one. Metabolomics has been widely used in the early toxicological screening of leads, preclinical and clinical toxicology of drugs in animals and human, as well as in surrogate models such as cell lines and zebrafish. Annotation techniques for metabolic data have also been developed. In this paper, the development of metabolomic techniques and its application in toxicology are reviewed.