Duodenal atresia is the frequent cause of neonatal intestinal obstruction. The association between duodenal atresia, intestinal malrotation, cardiac anomalies and Down syndrome is infrequently reported. We present a prenatally suspected case of duodenal atresia which was associated with malrotation and atrial septal defect in a patient of Down syndrome. Duodenotomy and resection of web was performed in addition to Ladd's procedure. Postoperative course remained uneventful.