Clear cell tumor (CCT) of the lung is very rare, and angiomyolipoma (AML) of the liver is also very rare. Both CCT and AML have been identified as a group of neoplasms with perivascular epithelioid cell differentiation (PEComa). We report a case with multiple PEComas of a combination of CCT of the lung and AML of the liver. The patient underwent surgical resection of an abnormal nodule of the lung 5 years after treatment of AML of the liver. The histological diagnosis of the pulmonary nodule was CCT. Neither lesion demonstrated malignant phenotypes, such as high mitotic activity, necrosis, or lymphovascular invasion. Each tumor of the lung and liver was solitary and differed from each other histologically. Therefore, these tumors were considered to be multifocal, not metastatic PEComas. This case is, to our knowledge, the first report of multiple PEComas of pulmonary CCT and hepatic AML. These findings suggest that patients with PEComas may require whole-body follow-up examinations because different subtypes of PEComas may occur multifocally.