This paper gives a brief history of the development of chemoinformatics since the first studies in the late 1950s and early 1960s of methods for searching databases of chemical molecules and for predicting their biological and chemical properties. Topics, and associated key papers, that are discussed include: structure, substructure, and similarity searching; the processing of generic chemical structures and of chemical reactions; chemical expert systems; the identification of qualitative and quantitative structure–activity relationships in both two and three dimensions; pharmacophore analysis; ligand–protein docking; molecular diversity analysis; and drug-likeness studies. Brief mention is also made of other important areas such as computer-assisted synthesis design and computer-assisted structure elucidation. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 46-56 DOI: 10.1002/wcms.1