The recovery of gastrointestinal function following surgery for congenital intestinal atresias can be prolonged and may increase morbidity and hospital stay. This study was conducted to investigate the prokinetic effect of erythromycin in neonates undergoing surgery for small bowel atresias. A randomized-controlled trial was conducted at the Departments of Paediatrics and Paediatric Surgery, Military Hospital, Rawalpindi, Pakistan, from January to December 2007 to study the prokinetic effect of erythromycin (3 mg/kg per dose 4 times daily). Thirty consecutive neonates undergoing primary anastomosis for congenital small bowel atresias were randomly divided into two groups: group I (erythromycin) and group II (control). The groups were similar in terms of gestational age, sex, mode of delivery, birth weight and types of atresias. Postoperative recovery of intestinal functions was measured as time taken to achieve full enteral feed (150 ml/kg per 24 h), duration of total parenteral nutrition (TPN) and hospital stay. Neonates receiving oral erythromycin achieved full enteral feeding early (13.07 vs. 16.13 days) required TPN for shorter duration (10.53 vs. 13.73 days) and their hospital stay was less (16.2 vs. 18.0 days) as compared to the neonates in the control group who did not receive any erythromycin. The differences were statistically significant. The administration of oral erythromycin following primary anastomosis for small intestinal atresias results in early recovery of intestinal function, fewer days on TPN and a trend for shorter hospital stay.