With the advent of ultrasonography (US), perinatal diagnosis of biliary cystic malformation (BCM) has become more prevalent. BCM includes cystic biliary atresia (CBA) and choledochal cyst (CC). Both share similar ultrasonographic features and clinical manifestations, and yet the postnatal management is very different. This study was to assess whether CBA can be distinguished from CC by US. We retrospectively studied the clinical data of 98 BCM patients aged less than 130days between January 2013 and November 2015. The patients were divided into the CBA group and the CC group based on intraoperative cholangiography. The ultrasonographic features in each group were then analyzed. Thirty-one children had CBA (type I: 24, type III: 7) and 67 children had CC (all: type I). The cyst volume did not show a significant change in the CBA group while the cyst volume increased postnatally in the CC group. Preoperative cyst volume can be used as a sensitive indicator to distinguish choledochal cyst from cystic biliary atresia. Gallbladder size in the two groups differed significantly (P = 0.034); 23 of 31 patients in the CBA group had atrophic gallbladder, whereas none of the patients in the CC group had atrophic gallbladder (P < 0.001). The triangular cord sign was detected in ten patients in the CBA group and in none of the patients in the CC group (P < 0.001). Serial prenatal and postnatal ultrasonographic studies may help differentiate CBA from CC in the majority of BCM, facilitating prenatal counseling and postnatal management.