Over the past decade, whole-genome scans have been used by academia and industry as an increasingly important tool in identifying genes of disease susceptibility. Genome coverage has improved dramatically, from sparse panels of hundreds or thousands of genetic markers five to ten years ago, to panels now comprising over 500,000 markers that capture more than 80% of the genetic information in the genome. Whole-genome scans have played a role in drug discovery, for which knowledge of the genes and gene pathways involved in disease susceptibility can be incorporated into the selection of drug targets. Such scans also have an important role in drug development, as the pharmaceutical industry shifts from a blockbuster strategy to a niche market approach; given that not all patients will receive benefit from a particular medication, genetic markers that predict efficacy can be used to identify subgroups of patients who display a significant therapeutic response. Similarly, genetic information can be used during the drug development and postmarketing stages to predict individuals who are at risk for an adverse event. At-risk patients can receive alternative therapies, while those individuals who are not at risk, and benefit from a given medication, can continue on the treatment regimen. This feature article discusses the use of whole-genome association scans in disease gene identification, drug discovery and development.