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This article reviews the current understanding and limitations in knowledge of the effect genetics and genetic diagnoses have on perioperative and postoperative surgical outcomes in patients with congenital heart disease (CHD). Presence of a known genetic diagnosis seems to effect multiple significant outcome metrics in CHD surgery including length of stay, need for extracorporeal membrane oxygenation, mortality, bleeding, and heart failure. Data regarding the effects of genetics in CHD is complicated by lack of standard genetic assessm