To relate omphalocele and biliary atresia and investigate possible embryological correlations that justify the simultaneous occurrence. A female preterm newborn diagnosed as omphalocele; cesarean delivery, weight 2,500g, 46 XX karyotype. Initially, the newborn remained fasting and on parenteral nutrition, and enteral diet was introduced later, with good acceptance. On the 12th day of life, the newborn presented direct hyperbilirubinemia, increased levels of liver enzymes and fecal acholia, with a presumptive diagnosis of biliary atresia. However, the ultrasound was inconclusive, due to anatomical changes resulting from omphalocele. A surgical approach was chosen on the 37th day of life aiming to confirm diagnosis of biliary atresia and to repair omphalocele. During the surgical procedure, structural alterations compatible with biliary atresia were observed, later confirmed by pathological examination; a hepatoportoenterostomy was performed and the omphalocele was corrected. She evolved well in the postoperative period, with a decrease in direct bilirubin and liver enzymes, as well as resolution of fecal acholia, and was discharged in good clinical condition. This is a bizarre and extremely rare association, but the prognosis may be good when an early diagnosis is made and surgery performed, besides support and clinical management to prevent complications in the perioperative period. Although the pathogenesis of the diseases has not been fully defined yet, there is, to date, no direct relation between them. The association between omphalocele and biliary atresia is extremely uncommon, with only two published cases.