Pharmacogenomics aims to elucidate the genomic determinants of drug disposition and effect. Because cancer chemotherapy is relatively nonspecific and has narrow therapeutic indices, there is great potential for pharmacogenomics to improve treatment outcomes by either reducing toxicity or increasing efficacy. The diversity of therapeutic targets for anticancer drugs and the intensity of clinical pharmacology research in oncology have provided many examples of clinically relevant pharmacogenomic applications. Important elements that are discussed in this article include the association of genetic variability in the metabolism, intracellular transport and targets of anticancer drugs. In addition, we summarize where the field stands currently, and how information from the host and tumor might be integrated into decision making.