Comparisons indicated that RASSF1A methylation, BVES methylation, AFP (≥20 ng/l) and HOXA9 methylation were the top 4 biomarkers for distinguishing HCC from CHB but that only RASSF1A methylation exhibited better sensitivity (52.0%) and specificity (91.5%) than AFP (48.0% and 73.9%, resp). Here, AFP is linked to hepatocellular carcinoma.