BACKGROUND Atresia of the jejunum and ileum is one of the major causes of neonatal intestinal obstruction. Most affected newborn infants present with bilious emesis and abdominal distention. Traditionally, jejunal and ileal atresia have been grouped together as jejunoileal atresia. OBJECTIVE To elucidate the difference between jejunal and ileal atresia. METHODS A retrospective analysis of patients diagnosed with jejunal or ileal atresia, who were treated at the Department of Surgery, Queen Sirikit National Institute of Child Health during January 1988 to December 2007, was carried out. RESULTS There were 74 patients with jejunal atresia and 68 patients with ileal atresia. The mean birth weight and gestational age of patients with jejunal atresia were significantly lower than those with ileal atresia. Antenatal perforation occurred more frequently in ileal atresia. Postoperative course was more prolonged and mortality was higher injejunal atresia. Prolonged ileus and anastomotic dysfunction requiring long-term parenteral nutrition were the major causes of complications leading to death. CONCLUSIONS There were many differences between patients with jejunal atresia and those with ileal atresia. The more compliant jejunal wall allows massive dilatation upon obstruction with subsequent loss of peristaltic activity, thus poorer outcome in comparison with ileal obstruction. We suggest that atresia of the jejunum and ileum be considered differently.