We present the case of a patient with biliary and duodenal atresia who showed false-negative hepatobiliary scintigraphy results. The patient was born at 37 weeks and 2 days of gestation. Her mother had undergone amnioreduction after detection of a double-bubble ultrasound sign in the fetal abdomen. At 2 days of age, total serum bilirubin level was elevated. On hepatobiliary scintigraphy 4 days later, the gallbladder was visualized from 30 min and it showed duodeno-gastric reflux at 240 min. After 24 h, the radiotracer was almost washed out in the hepatic parenchyma, but there was retention in the gastroduodenal junction. Because the biliary to duodenal transit was visible, biliary atresia seemed unlikely. Abdominal ultrasonography at 7 days of age showed a small dysmorphic gallbladder, but triangular cord sign was not definite. Magnetic resonance cholangiography revealed atretic gallbladder. Although cystic and common bile ducts were visible, the proximal common hepatic bile duct was not visible. The next day, serum total bilirubin levels remained elevated (17.1 mg/dl) with direct bilirubin level of 1.2 mg/dl. Kasai portoenterostomy with duodeno-duodenostomy was performed at 10 days of age. Histopathological evaluation showed a fibrous obliteration of the common bile duct, consistent with that of biliary atresia.