The ideal surgical management of neonates with necrotising enterocolitis (NEC) is still a matter of debate. The purpose of this study was to compare the results of bowel resection with primary anastomosis with the results of bowel resection with enterostomy. Sixty-three neonates with NEC had a bowel resection in the acute phase of the disease in the period between February 1990 and March 2001. Thirty-four of them (54%) underwent resection of the bowel with primary anastomosis (Group A), and 29 (46%) had resection with enterostomy (Group B). Group A had a lower gestational age and lower birth weight. Mortality, complication rate, and postoperative weight gain were not significantly different between the groups. However, Group B had a significantly longer primary hospital stay (80 +/- 49 days versus 58 +/- 31 days, P < 0.04) and needed a 2nd hospital stay for restoring gastrointestinal continuity. For both reasons, it can be argued that primary anastomosis is superior to enterostomy after resection.