Objective To determine the frequency of detection of cytomegalovirus (CMV) in surgical or autopsy intestinal tissue from infants with necrotizing enterocolitis (NEC) or spontaneous intestinal perforation (SIP) of the small bowel. Study design This was a retrospective cohort study of infants in the neonatal intensive care unit at Nationwide Children's Hospital, Columbus, Ohio, with NEC (Bell stage ³2B) or SIP from 2000 to 2016. Paraffin-embedded surgical or autopsy intestinal tissues were examined for CMV by polymerase chain reaction (PCR) and immunohistochemistry (IHC), and clinical characteristics of CMV-positive vs CMV-negative cases were compared. Results CMV was detected by PCR or IHC in 7 (4%) of 178 infants with surgical or autopsy-confirmed NEC (n = 6) or SIP (n = 1). Among 143 NEC cases (123 surgical, 20 autopsy), CMV was detected in 6 (4%): 4 (2 surgical, 2 autopsy) by both PCR and IHC, and 2 (surgical) by PCR only. Among 35 SIP cases (32 surgical, 3 autopsy), 1 (3%) surgical case was positive, by PCR only. CMV-associated NEC cases had lower median gestational age (24 vs 28 weeks; P = .02), birth weight (649 vs 1121 g; P = .04), and platelet count (16 000/mm 3 vs 50 000/mm 3 ; P = .018) compared with CMV-negative cases, respectively. No association was found with receipt of maternal milk, age at NEC diagnosis, male sex, cholestasis, or mortality. Conclusions CMV was detected in intestinal tissue from 4% of NEC or SIP cases (NEC, 4%; SIP, 3%). Lower gestational age, lower birth weight, and thrombocytopenia were significantly associated with detection of CMV in NEC or SIP cases.