Through an analysis of 2 databases, we describe outcomes among 11 958 neonates with congenital heart disease undergoing cardiac procedures, with 194 developing necrotizing enterocolitis (NEC). Neonates with congestive heart failure or those undergoing systemic to pulmonary artery shunting were more likely to develop NEC, but these patients had inpatient mortality similar to that of their non-NEC counterparts.