Abstract: A method of detecting hepatocellular carcinoma includes the steps of: detecting a methylation level of a CpG site of HOXA9 gene in a biological sample taken from a suspected subject; and comparing the methylation level to a reference methylation level of a CpG site of HOXA9 gene in another biological sample taken from a normal subject not suffering from hepatocellular carcinoma, wherein when the methylation level is higher than the reference methylation level, the suspected subject is likely to suffer from hepatocellular carcinoma, and wherein each of the biological samples is selected from the group consisting of a blood sample, a serum sample, and a plasma sample.