A rare case of clear cell variant of calcifying epithelial odontogenic tumor is presented with immunohistochemical and ultrastructural investigations. A 14-year-old Japanese girl was admitted with a complaint of swelling in the right posterior maxilla. Radiological examination showed a well-circumscribed radiolucent lesion located close to the impacted third molar. After only a partial tumor excision, the tumor recurred 13 years later. It appeared radiologically as an irregular radiodensity, and a subtotal maxillectomy was performed. Histological examination showed sheets and/or strands composed almost entirely of clear vacuolated epithelial cells in a stroma containing intercellular amyloid-like material and calcification. Histochemical and ultrastructural analysis detected cytoplasmic glycogen granules in the clear cells, and positive immunoreactivities for cytokeratins 8, 13 and 19; filaggrin and anti-ameloblastoma antibodies suggested an odontogenic epithelial origin.