<p>We report a rare case of thymoma with extensive clear cell components, and discuss the histogenesis of clear cell transformation. Although thymic clear cell carcinoma is classified as a subtype of thymic carcinoma, thymoma with extensive clear cell components has not been recognized as a subtype in the World Health Organization classification (2021). Therefore, such thymomas may be erroneously misdiagnosed as clear cell carcinoma. Thymic clear cell carcinomas are positive for glycogen, with a high Ki67 index, whereas the clear cell component of the present tumor was negative, with a low index; this difference may help to distinguish thymomas with extensive clear cell components from thymic clear cell carcinomas. In this tumor, spindle cells predominantly proliferated in the center, whereas clear cells were densely distributed in the periphery. Hence, the initial tumor likely consisted of spindle cells, some of which transformed into clear cells as the tumor grew larger. In addition, nuclei of the clear cells were occasionally positive for autophagy-related 4 cysteine peptidase. Electron microscopically, clear cells with eccentrically located nuclei and cytoplasm contained large vacuoles, in which irregularly shaped membranous structures were observed. The histology, immunohistochemistry, and ultrastructure suggest that clear cell transformation represents a type of cellular degeneration.</p>