Chemogenomics aims toward the systematic identification of small molecules that interact with the products of the genome and modulate their biological function. The establishment, analysis, prediction, and expansion of a comprehensive ligand–target SAR (structure–activity relationship) matrix has followed the elucidation of the human genome and presents a key scientific challenge for the twenty-first century. The anno- tion and knowledge-based exploration of the ligand–target SAR matrix is then expected to impact science greatly. Progress alongside this challenge without a doubt will c- tribute to further the fundamental understanding of the biological function of the individual proteins and ultimately provide a basis for the discovery of new and better therapies for diseases. While historically the chemogenomics approach is based on efforts that systematically explore target gene families, today broader in vitro and in silico approaches are available to encompass wider genomes. In this book, experts from academia and industry outline relevant aspects of ch- istry, biology, and molecular informatics which are the cornerstones of chemogenomics. General introductory chapters are combined with chapters describing methods and pro- cols, which are the gold standard of the Methods in Molecular Biology book series.