To review the bacteriology of neonatal intra-abdominal sepsis, we reviewed peritoneal cultures from 86 newborns undergoing operation for necrotizing enterocolitis (NEC) for the type and incidence of microorganism recovered. As a control, we conducted a similar review in 59 children with perforated appendicitis during the same period. Necrotizing enterocolitis was characterized by a lower incidence of polymicrobial contamination (1.7 organisms per patient vs 2.4 organisms per patient, NEC vs appendicitis) and an uncharacteristic pattern of isolates. Although enteric gram-negative bacilli were recovered in 80% of newborns, the incidence of Escherichia coli was only 21% in the NEC group vs 69% in the appendicitis group, while Klebsiella and Enterobacter species represented the most common gram-negative isolates recovered (63% vs 17%). More than 50% of neonatal cultures yielded gram-positive cocci, most frequently coagulase-negative staphylococci (30% vs 0%) and enterococci (17% vs 5%), as compared with more frequent streptococcal isolates in the appendicitis group (50% vs 10%). Anaerobes were seldom recovered in NEC cases (6%), but they were present in 50% of appendicitis cases. Additionally, Candida isolates were recovered in 10% of NEC cases (0% of appendicitis group). These results indicate the unique bacteriology of peritonitis in the critically ill newborn and probably reflect abnormal colonization in the neonatal intensive care unit.