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To evaluate and describe resource use and perioperative morbidities among those patients with genetic conditions undergoing cardiac surgery.Using the Pediatric Health Information System database, we identified patients ≤18 years old with cardiac surgery classified by Risk Adjustment for Congenital Heart Surgery (RACHS) during 2003-2014. A total of 95 253 patients met study criteria and included no genetic conditions (84.6%), trisomy 21 (9.9%), trisomy 13 or 18 (0.2%), 22q11 deletion (0.8%), Turner syndrome (0.4%), and “other” genetic conditions (4.2%). We compared perioperative complications and procedures in each genetic condition with patients without genetic conditions using regression analysis.All groups with genetic conditions, excluding trisomy 21 RACHS 3-5, experienced increased length of stay and cost among survivors. Complications varied by genetic condition, with patients with trisomy 21 having increased odds of pulmonary hypertension and nosocomial infections. Patients with 22q11 only had increased odds of infection. Patients with Turner syndrome had increased odds of acute renal failure (OR 2.35). Patients with trisomy 13 or 18 had increased odds of pulmonary hypertension (OR 3.13), acute renal failure (OR 2.93), cardiac arrest (OR 2.84), and nosocomial infections (OR 3.53), and those with “other” genetic conditions had increased odds of all complications.Children with congenital heart disease and genetic conditions, except trisomy 21 RACHS 3-5, had increased costs and length of stay. Perioperative morbidities were more common and differed across genetic condition subgroups. Patient-specific risk factors are important for risk stratification, benchmarking, and counseling with families.