AbstractProgression to cirrhosis despite restoration of bile flow by successful portoenterostomy suggests that factors other than obstruction alone are operative in biliary atresia. This paper describes pathologic changes at all levels of the hepatobiliary secretory apparatus from hepatocyte to common duct, exhibited in liver biopsies, resected portions of liver adjacent to the porta hepatis, and extrahepatic duct remnants from 17 patients operated upon for relief of biliary atresia. In both intra‐ and extrahepatic bile ducts, there were epithelial changes interpreted as occurring in a sequence of vacuolar degeneration, necrosis, inflammatory infiltration, and proliferative epithelial repair that precede obliterative fibrosis. From their distribution, it is inferred that these cytopathologic changes may not be simply due to distal obstruction. These ductal epithelial changes are similar to those that occur in livers of some patients with severe viral hepatitis. The association of these changes with giant cell transformation in all cases suggests that they reflect a common etiology for ductal and hepatocellular damage in the neonatal hepatitis‐biliary atresia spectrum. The persistence of these changes in liver biopsies following portoenterostomy suggests that they may be of pathogenetic significance in the progressive liver disease seen in most patients with biliary atresia.