Idiopathic adult ductopenia is very rare. We report one case in a 30-year-old man, whose clinical course was characterized by jaundice and pruritus. Laboratory investigations revealed cholestasis and polyclonal hypergammaglobulinemia. Serum antinuclear, antimitochondrial, and anti-smooth muscle antibodies and serological markers for viral hepatitis were negative. Endoscopic retrograde cholangiography showed no liver or biliary tract abnormalities. Histological examination of a liver specimen showed a vanishing bile duct syndrome and moderate portal infiltration with lympho-histiocytic cells; there were no granulomas. Liver transplantation was performed due to rapid development of cirrhosis. The differential diagnosis of idiopathic adult ductopenia with small duct primary sclerosing cholangitis, auto-immune cholangiopathy, and non syndromic paucity of intrahepatic bile ducts is unclear.