Reported herein is a case of benign clear cell tumor of the lung in a 60-year-old man. Chest X-ray and CT examination revealed an abnormal nodule with homogenous density and a clear margin in the lower lobe of the left lung. The resected tumor was 13 mm in size, well-circumscribed and was graysh-white on cut surface. Histological examination showed a diffuse growth pattern of polygonal tumor cells with indented and pleomorphic nuclei, and clear abundant cytoplasm with a distinct cell border surrounded by thin-walled vascular spaces and sinusoid-type vessels. The clear cytoplasm contained numerous glycogen granules as demonstrated by PAS staining. In the present case there was focal immunoreactivity for S-100 protein, HMB-45, neuron-specific enolase, cathepsin B and melan A, which are consistent with reported immunohistochemical staining patterns of benign clear cell tumor. Based on these findings, the tumor was diagnosed as a benign clear cell tumor of the lung. Although most clear cell tumors are considered to belong to the family of neoplasms with perivascular epithelioid cell differentiation (PEComas), histogenesis of benign clear cell tumor of the lung has remained unclear. This first report of CD1a expression in this tumor might provide a new insight into its histogenesis and diagnosis.