A case of clear-cell odontogenic tumor with unusual histological features is presented. A 61-year-old Japanese man was admitted because of swelling of the left premolar-molar region of the mandible. Radiological examination revealed a multilocular radiolucency with irregular margins. Histological examination of the resected specimen showed infiltrative proliferation of both clear and eosinophilic cells into the adjacent soft tissue without encapsulation, suggesting the malignant potential of the tumor. The tumor cells sporadically formed cystic lesions. In addition, several tumor cell nests showed duct-like characteristics, and many eosinophilic dentin-like structures were attached to the tumor cell nests, suggesting the potential for epithelial-mesenchymal induction. Histochemically, the clear tumor cells possessed cytoplasmic glycogen granules. Both clear and eosinophilic tumor cells showed positive immunoreactivities for cytokeratin 19, epithelial membrane antigen and filaggrin, indicating an odontogenic epithelial origin.