Clear-cell tumors of the head and neck are biologically diverse consisting of benign, malignant and metastatic lesions. These tumors pose a diagnostic challenge. In the oral cavity, these may be derived from odontogenic/nonodontogenic epithelium or from mesenchyme or can be metastatic. Odontogenic tumors with clear-cell change are rare. Calcifying epithelial odontogenic tumor (CEOT) is a rare, benign, locally aggressive odontogenic epithelial tumor affecting the jaw. Here, we report a case of clear-cell variant of CEOT with its histopathological differential diagnosis. A 43-year-old male patient with swelling in his lower right back tooth region showed a well-defined radiolucent lesion with smooth corticated periphery on radiograph. On incisional biopsy, tumor showed small sheets, cords and islands of odontogenic epithelium with nests of clear cells with no evidence of calcification. A final diagnosis of CEOT was established by differentiating other odontogenic and nonodontogenic lesions on the basis of clinical, radiographic, histopathologic and special stain features.