Small molecule natural products and synthetic compounds have long been developed and housed by pharmaceutical companies and biotechnology firms for drug discovery. In the past, academic scientists studied important biological processes and drug targets while industry developed drugs directed to these well-studied and validated targets. Recently, two major paradigm shifts in the field of small molecule drug discovery have occurred: 1) an expanded role for academia in drug discovery, and 2) an increased focus on developing small molecules as chemical tools for basic research. Academic institutions have now moved into the arena of small molecule drug discovery by establishing various centers or institutes with high-throughput screening (HTS) and medicinal chemistry capabilities. At the same time, bioactive small molecule compounds are being identified and characterized to serve not only as drug leads but also as molecular tools, or chemical probes, to elucidate principles of biological processes. These transitions are primarily driven by several major developments: 1) Complete sequencing and analysis of the human genome and subsequent comparative and disease genomics have revealed a large number of potential new drug targets, which also provides enormous opportunities for functional investigations; 2) Advances in combinatorial chemistry have made small molecule compounds, which once were exclusively proprietary property of private sectors, commercially available to academic institutions; 3) The cost of acquiring robots for laboratory automation and informatics has been significantly reduced, thus making these essential resources accessible to academic investigators; and 4) Recognition of the tremendous potential of these unique opportunities and subsequent investment by various academic institutions and the National Institutes of Health (NIH) has catalyzed this transition from an almost exclusively industrial endeavor to an academic pursuit. Today, the concept that academic institutions have the ability to discover active small molecule compounds and use them to decipher the function of important biological processes has become a reality. These advances have greatly accelerated the development of the chemical biology field and have allowed scientists to harness the power of chemistry to elucidate biological processes and transform medicine.