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A case of anal canal neuroendocrine carcinoma with Pagetoid intraepithelial extension is presented. An 80-year-old man was admitted to hospital with a complaint of pain in the anorectal region. Clinical examination revealed a hard and fixed mass in the anal canal, and subsequent biopsy of the lesion showed it to be a carcinoma. The surgically resected specimen showed a solid tumor measuring 3.4 × 3.2 cm within the area from the surgical anal canal to the anatomical anal canal. Tumor cells proliferated predominantly with compact nests. Many tumor cells had a high nuclear-to-cytoplasmic ratio, dispersed chromatin, and conspicuous nucleoli. Additionally, neoplastic cells focally formed a glandular structure. Some polygonal neoplastic cells were small with round nuclei. A rosette-like arrangement was also focally observed. In addition, tumor cells exhibited Pagetoid extension into the overlying epithelium of the histological anal canal. Both the underlying original neoplastic cells and the Pagetoid spreading tumor cells showed cytoplasmic granules positive for Grimelius staining and immunopositivity for carcinoembryonic antigen, synaptophysin and cytokeratins 7 and 20. These findings are highly suggestive of neuroendocrine differentiation of adenocarcinoma cells. To the best of our knowledge, this is the first case of anal canal neuroendocrine carcinoma with Pagetoid extension into the overlying epithelium of the histological anal canal.