Necrotizing enterocolitis (NEC) and isolated intestinal perforation (IP) are two relatively common disease conditions that require neonatal surgical therapy. The early mortality rate approaches 50%, and survivors frequently have growth and neurodevelopmental impairment. Much discussion has occurred regarding whether initial drain placement alone or laparotomy with resection of diseased intestine should be the initial surgical therapy. Several recent prospective studies have shown that the early mortality rate is likely not significantly different after either of these surgical approaches. Major morbidity, especially the likelihood for neurodevelopmental impairment, may be different in the two treatment groups. Further prospective trials are needed to further explore this question and are planned. Studies focusing on prevention of NEC and IP and also on improved medical treatment are needed to allow a major advance in the outcomes of infants with NEC and IP. As these studies are being performed, trials evaluating existing medical and surgical therapies are also needed.