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BACKGROUND/PURPOSE The gastrointestinal system is prone to complications following heart surgery. We sought to determine the incidence and factors associated with gastrointestinal complication after cardiac surgery in children. METHODS A retrospective review of patients aged <16years that underwent cardiac surgery between 2009 and 2013. Primary outcome was occurrence of gastrointestinal complication within 30days. Multivariable logistic regression was performed to identify variables related to occurrence of gastrointestinal complication. Patients with gastrointestinal complication were matched with controls and postoperative lengths of stay compared. RESULTS Eight hundred eighty-one children underwent 1120 cardiac surgical procedures. At time of operation, 18% were neonates and 39% were infants. Cardiopulmonary bypass was used in 79%. Of 1120 procedures, 31 (2.8% [95% CI 2.0-3.9%]) had gastrointestinal complication. Necrotizing enterocolitis accounted for 61% of complications. Of patients with gastrointestinal complication, 87% survived to hospital discharge. Gastrointestinal complication was associated with preoperative co-morbidity (OR 2.2 [95% CI 1.02-4.8]) and univentricular disease (OR 2.5 [95% CI 1.1-5.5]). Neonates had the highest risk of gastrointestinal complication. Patients with gastrointestinal complications had longer hospital stays than controls (median difference, 13days [95% CI 3-43]). CONCLUSIONS Serious gastrointestinal complications are uncommon but associated with longer hospital stay. Neonates with univentricular disease and preoperative comorbidity are at highest risk. TYPE OF STUDY Prognosis study. LEVEL OF EVIDENCE II.