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Primary mucosa-associated lymphoid tissue (MALT) lymphomas rarely originate in the hilar bile duct. Preoperative diagnosis of a primary MALT lymphoma of the hilar bile duct is difficult owing to the rarity of this disease. Differentiating between obstructive jaundice caused by MALT lymphoma of the hilar bile duct and hilar cholangiocarcinoma (the most common form of bile duct cancer) is challenging.A 57-year-old man presented to our hospital in August 2012 with fluctuant obstructive jaundice.Contrast-enhanced abdominal computed tomography and magnetic resonance cholangiopancreatography showed a hilar liver mass measuring 23 × 28 mm along with intrahepatic biliary dilatation indicating hilar bile duct obstruction with a high index of suspicion for hilar cholangiocarcinoma.Based on frozen section examination, he was intraoperatively diagnosed with chronic nonspecific inflammation. Histopathological and immunohistochemical examinations confirmed a diagnosis of malignant lymphoma, specifically classified as an extranodal marginal zone B-cell lymphoma of MALT type.A primary MALT lymphoma of the bile duct should be considered among the differential diagnosis in patients with a hilar tumor who present with fluctuating jaundice and are preoperatively diagnosed with suspected hilar cholangiocarcinoma, and/or an intraoperative diagnosis of chronic nonspecific inflammation (based on frozen section examination) assessed for stenosis or obstruction of the bile duct.