Because it is difficult to distinguish preoperatively between prenatally diagnosed choledochal cyst (CC) and type I cystic biliary atresia (BA) by ultrasound scanning or magnetic resonance imaging (MRI), some modality of discrimination for the 2 entities is required. The aim of this study was to investigate the histological differences between prenatally diagnosed CC and type I cystic BA using liver biopsy specimens. Four children with prenatally diagnosed CC and two children with prenatally diagnosed type I cystic BA were identified by fetal ultrasonography between 1985 and 2003. The control group included two children who were operated on at an earlier period due to postnatally diagnosed BA. Liver wedge biopsy in the right lobe was performed at the time of the radical operation. Histological findings of the H & E-stained liver biopsy specimens were classified into 4 grades (Grade 0, no abnormality; Grade 1, ductular proliferation without bridging fibrosis; Grade 2, ductular proliferation with bridging fibrosis; and Grade 3, liver cirrhosis). The CC group consisted of one case of Grade 0 and three cases of Grade 1. The type I cystic BA group consisted of one case each of Grade 2 and Grade 3. In the control group, both cases were Grade 2. The authors suggest that exploratory laparotomy might be avoided and, instead, histologic examination using liver biopsy specimens can be a reliable test for the differential diagnosis of CC and type I cystic BA in prenatally diagnosed neonates.