An important component of drug discovery is the storage, searching, and manipulation of chemical structures and reactions. Over the past three decades, the science of chemical information management has grown along with advances in computer hardware, software, and database systems. This chapter discusses the evolution of chemical information storage in the corporate environment, from flat files to specialized databases to relational database systems. An example methodology for storing and searching structures in a relational database system is described. The recent deluge of information from high throughput chemistry is leading to the appearance of chemical data marts, data warehouses, and structural data mining, which are briefly discussed. Finally, a short look is taken into the future of chemical information and knowledge management, with respect to databases, software, and hardware. This review focuses on chemical structure database management. Other chapters describe the generation of chemical structures and their properties and the use of this data in the drug discovery process.