Many neuropsychiatric disorders of childhood and adolescence have a strong genetic component, and all present challenging questions about the neural abnormalities that underlie complex and unique behavioral and cognitive phenotypes. A useful research strategy in this setting is imaging genetics, a relatively new approach that combines genetic assessment with multimodal neuroimaging to discover neural systems linked to genetic abnormalities or variation. In this article, the authors review this strategy as applied to two areas. First, the authors present results on dissecting neural mechanisms underlying the complex neuropsychiatric phenotype of Williams syndrome. Second, they examine neural systems that are linked to candidate gene genetic variation that mediate risk for psychiatric disorders in a gene by environmental interaction. These data provide convergent evidence for neural circuitry mediating emotional regulation and social cognition under genetic control in humans.