Neonatal hepatitis(NH) and congenital extrahepatic biliary atresia(BA) are two major causes of neonatal cholestasis. The method of therapeutic trials for each disease is essentially different. Nonetheless it is very difficult to differentiate these diseases histologically, since most of the hepatic changes are mutual in both of them. This study is to aimed to find out major differences between the two by scoring various histological parameters. A total of 63 consecutive liver biopsies taken from 54 patients with suggested NH and BA were examined by applying morphometric scoring system. The detailed clinical histories, laboratory data including serology for HBsAg and TORCH infection and radiologic operative findings were reviewed. Among 54 patients, 27 were diagnosed as NH and 20 as BA. In two cases, features of both diseases were coexistent. The pathological diagnosis was not compatible with the final diagnosis in 5 cases(10.7%). In all of these 5 cases, biopsy had been performed at the age of one to two months. The seropositivity for TORCH was 59.3%(16.27) in NH, but 25.0%(5/20) in BA. Serum AST, ALT and alpha-fetoprotein values were higher in NH, and total bilirubin in BA. Of various histological parameters, scores of portal fibrosis, bile duct and ductular proliferation and bile thrombi were much higher in BA, and at the age of less than 2 months, extramedullary hemopoiesis(EMH) was found much more frequently in NH. Giant cell transformation of hepatocytes(GCT) was more commonly observed in NH. The numbers of GCT and EMH were particulary plentiful when the patients' sera were positive for HBsAg or TORCH. These results indicate that portal fibrosis, biliary proliferation and bile thrombi are the three major histologic features of BA, and therefore erroneous histological diagnosis may ensue when scores of those features are low as in some early BA.