A 78-year-old woman with a chief complaint of mammary tumor was referred to our hospital and was diagnosed with mucosa-associated lymphoid tissue (MALT) lymphoma using needle biopsies. She presented with MALT lymphoma lesions in the stomach, duodenum, and intraperitoneal lymph nodes. Abdominal ultrasonography revealed thickened internal layer of the bile duct. Cholangiocarcinoma, immunoglobulin G4-related sclerosing cholangitis, and MALT lymphoma were suspected. She did not report any abdominal pain, and did not have jaundice. Endoscopic retrograde cholangiopancreatography and intraductal ultrasonography indicated diffuse, irregular wall thickening with the formation of nodule lesions in the extrahepatic bile duct. Transpapillary cytology indicated CD20-positive atypical lymphocytes. MALT lymphoma of the bile duct was diagnosed. CVP with rituximab therapy was performed. After treatment, computed tomography, gastrointestinal endoscopy, endoscopic retrograde cholangiopancreatography, intraductal ultrasonography, and transpapillary cytology revealed that the tumor and the biliary wall thickening had disappeared. It is difficult to diagnose MALT lymphoma of the bile duct. We report a case in which intraductal ultrasound and transpapillary cytology were useful for establishing a diagnosis and evaluating the therapy for MALT lymphoma of the bile duct.