Because it is difficult to distinguish preoperatively between a prenatally diagnosed choledochal cyst (CC) and type-1 cystic biliary atresia (BA) by ultrasound scanning or magnetic resonance imaging, some mode of discriminating between the 2 entities is required. The aim of this study was to investigate the immunohistological differences between prenatally diagnosed CC and type-1 cystic BA, using liver biopsy specimens immunostained for CD56. Five children with prenatally diagnosed CC and two children with prenatally diagnosed type-1 cystic BA were identified by fetal ultrasonography between 1985 and 2004. 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 CD56-stained liver biopsy specimens were classified into 4 categories each, with particular focus on staining distribution and intensity. The staining distribution was classified according to the scale 0 = no staining; 1 = some staining of bile ducts/ductules but staining in less than one-third of portal tracts; 2 = staining in one-third to less than two-thirds of portal tracts; and 3 = staining in more than two-thirds of portal tracts. Staining intensity was scored as follows: 0 = no staining, 1 = weak staining, 2 = moderate staining, and 3 = strong staining. The staining intensity and distribution in the CC group was zero in all 5 cases. The type-1 cystic BA group consisted of patients with scale 1 or 3 staining distribution and score 1 or 2 staining intensity. In the control group, staining distribution was 1 or 3, and staining intensity was 1 or 3. These results indicate that CD56-positive biliary duct cells are present in prenatally diagnosed type-1 cystic BA. The authors suggest that exploratory laparotomy might be avoided and, instead, immunohistological examination using liver biopsy specimens may be a reliable test for the differential diagnosis of CC and type-1 cystic BA in prenatally diagnosed neonates.