Mucosa-associated lymphoid tissue lymphoma of the extrahepatic bile duct has not yet been reported. Much more common than this is secondary involvement of the extrahepatic bile duct in cases of disseminated lymphoma. A 59-year-old man manifesting jaundice was referred to our hospital. PTC revealed an extrahepatic bile duct stenosis from the hilum to the lower part of the choledochus. On the operative specimen, we examined L26/CD20, Bcl-2, UCHL-1/CD45RO, cyclin D1 and p53. Histologically, follicular colonization, centrocyte-like cells and lymphoepithelial lesion was observed. Tumor cells were positive for L26/CD20 and Bcl-2 and were negative for intracytoplasmic immunoglobulins, UCHL-1/CD45RO, cyclin D1 and p53. Pathological diagnosis was mucosa-associated lymphoid tissue lymphoma of the extrahepatic bile duct. The authors present herein the first case of mucosa-associated lymphoid tissue lymphoma of the extrahepatic bile duct. It was very difficult to distinguish from hilar cholangiocarcinoma clinically. Only incomplete stenosis of the bile duct and 18-F fluoro-2-deoxyglucose positron emission tomography (FDG-PET) could suggest this unusual clinical entity.