Ensuring confidentiality and privacy is vital for databases containing individual-level genotype or phenotype information. Important concerns about the potential for persons carrying risk-associated variants (i.e., essentially everyone) becoming the object of discrimination by employers or insurers must be addressed. Application of GWA findings and other genomic research will be greatly facilitated by the formal legal protection against discrimination based on genetic information provided by the Genetic Information Nondiscrimination Act (GINA) that was signed into law in May 2008. When it goes into effect in 2009, GINA will protect against discrimination by health insurers and employers on the basis of genetic information. It is particularly important for GWA studies because of the breadth of information obtained in such studies; almost certainly every individual will carry at least one risk allele for at least one common disease. Protections under GINA will not only shield study subjects from the risk of genetic discrimination due to their participation in research, but more importantly will ensure that clinicians can order genetic tests identified from GWA studies to make more effective treatment decisions and can place this information in patients’ records without risk to patients or their families.