The large number of sequence variations in human genes reflects the diversity of human populations and the response to prior environmental and pathogen challenges. Currently, major efforts are under way to identify and catalog single-nucleotide polymorphisms for use in genetic studies designed to explore the contribution of common variants to both disease susceptibility and interindividual differences in outcomes. So far, the most productive approach has been to search with candidate genes for which there is a scientific rationale (eg, prior data on the biologic implications of one or more variant alleles). Recently, there has been an explosion in the number of genetic association studies seeking to correlate one or more well-defined outcomes with variant alleles. These studies provide a foundation for identifying and applying genetic risk factors to clinical medicine. However, a number of challenges must be met before widespread use in clinical medicine can be undertaken. These include more efficient bioinformatics, basic insights into the significance of the variant alleles, ethical issues, and the availability of cost-effective, high-throughput platforms for genotype analysis.