Genetic diversity, including single nucleotide polymorphisms, contributes to both disease susceptibility and variability in drug response. Since most genes contain multiple single nucleotide polymorphisms, identifying those that are most relevant with respect to disease or drug response is important and may uncover variants that are predictive of either disease susceptibility or therapeutic response to drugs, both with respect to efficacy and toxic side effects. The candidate gene approach has been widely used to search for the genetic basis of pharmacogenomic traits. Although a few successful examples have emerged from this approach, notably trastuzumab (Herceptin; Genentech), imatinib mesylate (Gleevec (USA), Glivec; Novartis) and certain drugs that demonstrate variable efficacy or adverse effects that are attributed to metabolizing enzymes, for most drugs, the genetic variations that determine their clinical response remain uncovered. Genome-wide linkage approach presents an alternative to the candidate gene approach. The powerful combination of linkage when coupled to ultra-high-throughput genotyping, gene array and proteomics technology, together with innovative bioinformatic resources, provides a focused integrative strategy for pinpointing disease-causing genes that may generate validated drug targets and genes that are responsible for differential drug response. Thus, it is anticipated that genetic research will soon generate new information that can be used to develop novel therapeutic strategies and diagnostic tests that will ultimately lead to safer and more efficacious drugs for all patients. This review addresses recent advances in the development of genetic markers that can be used to diagnose disease or drug response.