Population substructure and recent admixture may confound the results of genetic association studies in unrelated individuals, leading to a potential excess of both false positive and false negative results. The possibility of false associations depends on the population sampled, the trait being studied and the marker being tested. Although family based tests of association avoid the possibility of confounding due to population substructure and admixture, association studies in unrelated individuals may be preferred in many situations due to their feasibility. Unlinked genetic markers may be used to detect confounding in association studies. In addition, the information from unlinked markers may be used to adjust genetic associations.