Significant noncardiac and genetic abnormalities (NC and GA) are common in neonates with congenital heart defects. We sought to examine current-era effect of those abnormalities on early and late outcomes following cardiac surgery. The method from 2002-2012, 1538 neonates underwent repair (n = 860, 56%) or palliation (n = 678, 44%) of congenital heart defects. Regression models examined the effect of NC and GA on operative results, resource utilization, and late outcomes. Neonates with NC and GA (n = 312, 20%) had higher incidence of prematurity (21% vs 13%; P < 0.001) and weight =2.5kg (24% vs 12%; P < 0.001) than neonates without NC and GA (n = 1226, 80%). Although the incidence of single ventricle was comparable (34% vs 31%; P = 0.37), neonates with NC and GA underwent more palliation (52% vs 42%; P = 0.001) and subsequently had higher percentage of STAT mortality categories (Society of Thoracic Surgeons (STS) and the European Association for Cardio-thoracic Surgery (EACTS) Congenital Heart Surgery Mortality Categories) 4 and 5 procedures (78% vs 66%; P < 0.001). Adjusted logistic regression models that included disparate patient and operative variables showed that the presence of NC and GA was associated with increased unplanned reoperation (odds ratio = 1.7; 95% CI: 1.1-2.7; P = 0.03) and hospital mortality (odds ratio = 2.2; 95% CI: 1.3-3.6; P = 0.002). Adjusted linear regression models showed significant association between NC and GA and increased postoperative mechanical ventilation duration, intensive care unit, and hospital stays (P < 0.001 each). Adjusted hazard analysis showed that the presence of NC and GA was associated with diminished late survival (hazard ratio = 2.4; 95% CI: 1.9-3.1; P < 0.001) and that was evident in all subgroups of patients (P < 0.001 each). Conclusion is neonates with NC and GA commonly have associated risk factors for morbidity and mortality such as prematurity and low weight. After adjusting for those factors, the presence of NC and GA continues to have significant association with increased unplanned reoperation, hospital mortality, and resource utilization after palliative and corrective cardiac surgery. Importantly, the hazard of death in those patients continues beyond the perioperative period for at least 1 year. Our findings show that the presence of NC and GA should be emphasized during parent counseling and decision making; and underscore the need to explore strategies to improve outcomes for this high-risk population that must address perioperative care, outpatient surveillance, and management.