The prognosis of extrahepatic biliary atresia (EHBA) and multiple apparently not linked anomalies has never been disclosed. We reported a rare case affected by biliary, anorectal and esophageal atresia, and collected the uncommon associations of EHBA with multiple unrelated congenital defects to make known the prognosis. An elevated rate of hepatic failure despite surgery and an early poor outcome were found in the above-mentioned associations. A liver transplantation at the first months of life could be considered to improve outcome.