In a patient with a small endocrine carcinoma of the rectum, an unusually large lymph node metastasis was the only preoperative clinical finding. Low anterior rectal resection with total mesorectal excision and lymph node dissection was performed. The tumor demonstrated some highly unusual characteristics: it was classified as a small, low-grade neuroendocrine rectal carcinoma of L-cell type with three large lymph node metastases and morphological consistency with an endocrine tumor and focal positivity of glicentin, demonstrating a proliferation of smooth muscle cells. The established Capella classification of endocrine tumors of the rectum by morphological findings would have characterized this primary tumor as benign. In this case, however, clinical and histopathological findings more accurately reflected its malignant potential.