Necrotizing enterocolitis (NEC) is the most common gastrointestinal emergency in neonates and is associated with significant morbidity and mortality. An association between HIV-positive maternal status and increased risk of NEC in preterm infants has been described, and antiretroviral therapy has been proposed as an independent risk factor. Our aim was to compare the clinical presentation and histopathological features of necrotizing enterocolitis in HIV-exposed and unexposed infants. A retrospective study of archival material from the National Health Laboratory Services Histopathology Laboratory in Tygerberg Hospital/Stellenbosch University from 1992 to 2008 was conducted. All surgical specimens from infants who presented to pediatric surgery for a laparotomy and bowel resection for NEC and in whom the HIV status was known were included in the study. In the 37 cases that fulfilled these criteria, male gender was overrepresented in the study population (67%). Nonsteroidal anti-inflammatory drugs appeared to play a significant role in the development of surgical NEC in infants who were not exposed to HIV, but HIV-exposed infants had a significantly poorer survival rate. There was no significant difference in the histopathology between HIV-exposed and nonexposed infants, and Cytomegalovirus infection was not identified in any of the cases studied.