Infants with CHD are at increased risk of necrotising enterocolitis, which can interfere with the achievement of adequate nutrition and, ultimately, growth and development. Necrotising enterocolitis is classified by severity as suspected, confirmed, and advanced. We sought to quantify the incidence of all types of necrotising enterocolitis among infants who underwent surgery, with a particular focus on suspected necrotising enterocolitis. This is a retrospective review of all infants <6 months of age who underwent cardiac surgery during 2012 and 2013 at Children’s Hospital Colorado. We examined the hospital course of 265 hospitalisations (n=251 patients) and found 18 patients (19 hospitalisations) with suspected necrotising enterocolitis and 16 patients (16 hospitalisations) with confirmed or advanced necrotising enterocolitis. Single-ventricle physiology, lower weight, and younger age were associated with necrotising enterocolitis. Patients with all types of necrotising enterocolitis experienced prolonged length of hospital stay. We found suspected necrotising enterocolitis to be as common as confirmed necrotising enterocolitis, and it frequently occurred early in the post-operative course. We speculate that suspected necrotising enterocolitis may often be overlooked in research owing to a reliance on billing codes. Nevertheless, suspected necrotising enterocolitis poses a substantial barrier to post-operative progression of the CHD patient, as does confirmed necrotising enterocolitis. Following the diagnosis of all types of necrotising enterocolitis, there was wide variability in practice patterns. In response to this variability, we developed care guidelines for the diagnosis and treatment of necrotising enterocolitis in this population.