Autoimmune pancreatitis is a recently proposed disease entity. It is sometimes associated with other inflammatory diseases such as Sjögren's disease and sclerosing cholangitis. We report here a case of autoimmune pancreatitis associated with sclerosing cholangitis. The patient was a 74-year-old Japanese male who presented with obstructive jaundice and mild epigastric pain. Computed tomography scan and magnetic resonance cholangiopancreatography showed a diffuse swollen pancreas and poor visualization of the main pancreatic duct. The distal bile ducts were stenotic with marked dilatation of the main and intrahepatic bile ducts. Consequently, a pylorus preserving pancreatoduodenectomy was performed because bile duct carcinoma could not be ruled out. Pathological findings of the removed tissues showed fibrosis with lymphoplasmacytic infiltration in both the choledochus and pancreas head, destruction of pancreatic acinar tissues and obliterative phlebitis. Postoperative laboratory studies showed elevated serum IgG and detection of antinuclear factor. Scattered IgG4-positive plasma cells detected by immunohistochemistry appeared in the pancreas and in the periductal region of the bile duct. This case was finally diagnosed as autoimmune pancreatitis associated with sclerosing cholangitis.