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Small bowel atresia constitutes congenital obstruction of the lumen of the duodenum, jejunum or ileum, and is one of the most common causes of neonatal bowel obstruction with a reported incidence of between 1.3 and 2.8 per 10,1000 live births. Complete absence of the small bowel, or near total jejuno-ileal atresia (in the absence of malrotation or gastroschisis), are extremely rare. Mid-trimester prenatal sonographic finding of dilated fetal bowel led to the finding of interstitial 8q21.13q21.2 duplication. Following delivery at 32 weeks’ gestation, at laparotomy almost complete small bowel atresia was noted. Anastomosis between the existing small bowel and colon was performed. At 7 months of age, the infant continued to receive total parenteral nutrition supplemented by gastrostomy and oral-spoon formula feeding, and weighed 7 kg (50th centile). This is the first report of the association interstitial 8q21.13q21.2 duplication, which includes OMIM genes (RALYL, LRRCC1, and E2F5) and extensive small bowel atresia.