A rare case of clear cell odontogenic tumor is presented with an immunohistochemical study using epithelial cell markers. A 35-year-old Japanese man was admitted with a complaint of painless swelling in the anterior region of his mandible. Radiological examination showed a relatively well-defined multilocular radiolucency with root resorption of the adjacent teeth. Despite a subtotal mandibulectomy, the tumor recurred three times. Histologically, the tumor was composed of proliferating clear cells and infiltrated through the cancellous bone. Histochemical and ultrastructural analyses detected cytoplasmic glycogen granules in the clear cells. They showed immunoreactivities for cytokeratin 8, 13 and 19, filaggrin and anti-ameloblastoma antibodies, suggesting an odontogenic epithelial origin.