In HCC patients, the prevalences of hypermethylation for RASSF1A, APC, BVES, HOXA9, GSTP1, and TIMP3 were 52.04%, 36.73%, 29.59%, 20.41%, 17.35%, and 11.22%, respectively, and APC methylation completely overlapped with RASSF1A methylation. Here, HOXA9 is linked to hepatocellular carcinoma.