Metabolomics is being used in Drug Discovery and in development from lead compound discovery to post approval drug surveillance. A consequence of disease leads to metabolic changes. These changes are the cause of disease advancement. Metabolomics can help in finding potential new sites for therapeutic intervention by identifying metabolic changes. Metabolomics can provide activity information about possible novel drugs and drug scaffolds, indicate interesting targets for drug development and suggest binding partners of compounds. Furthermore, metabolomics can be used for the discovery of novel natural products and in drug development. Metabolomics can enhance the discovery and testing of new drugs and provide insight into the on- and off-target effects of drugs.