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Chemogenomics is the systematic genome-wide study of the cellular response to small molecule agents. Modern high-throughput genetic techniques allow massively parallel examination of the genetic effects of such biologically active small molecules (BASM). Here we present methodology for the identification and characterization of potentially bioactive compounds using the budding yeast Saccharomyces cerevisiae as a model organism. First, we present a method for screening libraries of compounds for growth inhibition in solid or liquid phase, followed by techniques for potency determination using a half-log dose response. Then the Deletion Mutant Array (DMA), a genome-wide library of single gene deletion strains, is used to probe the chemical genetic interactions of individual BASMs on genetic networks-a process that can be achieved with a solid phase pinning assay or a pooled liquid assay utilizing barcode microarray techniques. Finally, we offer some considerations for optimizing these protocols.