PURPOSE: Neonatal hepatitis and congenital extrahepatic biliary atresia are two major causes of neonatal cholestasis. But the method of therapeutic trials used for each disease is essentially different. Nonetheless, it is very difficult to differentiate these diseases clinically and histologically. This study is aimed to find out major differences between the two by clinical characteristics and scoring of various histological parameters. METHODS: Clinical and histologically assessments were carried out in 8 cases with neonatal hepatitis and 11 cases with extrahepatic biliary atresia, who were admitted to the Department of Pediatrics, Pusan National University Hospital, from January 1991 to June 1997. RESULTS: By sex distribution, males were more commonly had neonatal hepatitis but females were more commonly had biliary atresia. Hepatosplenomegaly and acholic stool were more frequent in biliary atresia.. Serial determinations of serum bilirubin concentrations showed that a steady fall occured in neonatal hepatitis whereas, progressive increase or stability of bilirubin level was noted in biliary atresia. Serum direct bilirubin level of more than 4mg/dL was found more frequently in biliary atresia. Serum aspartate aminotransferase level above 400IU/L was found more frequently in biliary atresia. Bile duct proliferation was more frequent in biliary atresia but Kupffer cell proliferation was more frequent in neonatal hepatitis. There was a significant difference in the total score in the liver biopsy scoring system between the two diseases. CONCLUSION: Females with hepatosplenomegaly and acholic stool, serum direct bilirubin level higher than 4mg/dL, serum aspartate aminotransferase level above 400IU/L, prominent bile duct proliferation and a higher total pathological score in biopsy specimen was found more frequently in biliary atresia.