To differentiate at ultrasonography (US) between the choledochal cyst associated with biliary atresia (CCBA) and that in the absence of biliary atresia (CC) in neonates and young infants. Preoperative US findings in 28 neonates and infants younger than 4 months in whom choledochal cyst was subsequently surgically confirmed were retrospectively analyzed. There was no statistically significant difference in age between the CCBA group (n = 19) and the CC group (n = 9). US findings in both groups were compared, with focus on the size of the cyst in the hepatic portal, dilatation of the intrahepatic bile ducts, and the size and morphology of the gallbladder. At US, the width and length of the cysts in the hepatic portal in the CC group were significantly larger than those in the CCBA group (P < .001). Dilatation of the intrahepatic bile ducts, seen in only one patient (5%) of the CCBA group, was observed in all patients (100%) of the CC group. The gallbladder was normal or distended in all patients of the CC group, while it was atretic or irregularly elongated in 17 patients (89%) of the CCBA group. US can be helpful in the preoperative differential diagnosis of choledochal cysts in neonates and infants. Cysts are larger, intrahepatic ducts are dilated, and gallbladders are not atretic in patients with CC as compared with those in patients with CCBA.