Clear cell hepatocellular carcinoma (HCC) is an uncommon variant of HCC. It is considered to have a better prognosis than non-clear cell HCC, but recent large studies show that there is some controversy. DNA image cytometry reveals diploid and non-diploid DNA content tumors that have different pleomorphisms and mitosis corresponding to different prognoses. Clear cell HCC is classified as focal or diffuse. Herein, we report a rare case of a 61-year-old male with two adjacent hyper- and hypoechoic hepatic nodules and an alpha-fetoprotein concentration of 6,370 ng/mL. Pathologic examination of a specimen obtained during wedge hepatectomy showed both clear cell and non-clear cell HCC. Bone metastasis was later found. We suggest that a patient with clear cell HCC should be followed up closely after complete resection.