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Extrapulmonary primary small cell carcinoma comprises approximately 4% of all small cell carcinoma. In the common bile duct, small cell carcinomas are extremely rare. We experienced a 60-year-old woman with small cell carcinoma arising in the common bile duct. Abdominal CT scan revealed an intraluminal mass in the proximal common bile duct and multiple lymphadenopathies. Microscopic examination of the tumor revealed proliferation of small monotonous anaplastic cells, which were characterized with hyperchromatic nuclei, high nuclear to cytoplasmic ratio, and frequent mitosis. By immunohistochemical stain, the tumor cells were strongly positive for chromogranin, synaptophysin, and CD56. We report this case with a review of literatures.