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Combinatorial chemistry is being applied to diverse problems in the biological and pharmaceutical sciences. This review will describe an emerging application called "chemical genetics" or "chemical genomics" - genetics and genomics are often used interchangeably in this context. In forward chemical genomics, chemical libraries are tested in living systems to discover compounds that cause a desirable effect. Subsequently, the protein target is identified using various biochemical and molecular biological tools. By this method, we gain insights into the inner workings of life, and indeed, in some forms this has been the path by which most of the pharmacopoeia was discovered. In reverse chemical genetics, proteins of interest are used to probe compound collections, and those compounds that bind the proteins of interest are used to treat living systems and observed for interesting biological responses. Plausible biological roles of these proteins are inferred from the effects of the compounds because they are assumed to generally inhibit, or more rarely, stimulate, the protein's functions. Interestingly, the reverse genetic approach is emerging as the leading model for drug discovery today. Different methods and cases will be described to illustrate forward and reverse paradigms, including those developed in the author's laboratory.