We performed this study to investigate whether serum cell-free DNA testing(liquid biopsy)of either methylated SEPT9 or methylated SST, which are possible biomarkers of HCC, in combination with AFP may improve clinical performance for the detection of HCC. Study subjects included 25 healthy controls, 15 patients with chronic liver disease without HCC, and 38 patients with HCC. Methylation level of serum cell-free SEPT9 and SST was measured by methylation-sensitive restriction enzymes followed by multiplex droplet digital polymerase chain reaction. According to receiver operating characteristic curve analysis to discriminate between non-HCC group(including control group and chronic liver disease without HCC group)and HCC group, area under the curve(AUC)was 0.73 by AFP and 0.73 by mSEPT9, whereas it was only 0.59 by mSST. Regarding combination tests, although negative predictive values were almost same between the AFP + mSEPT9 test and the AFP + mSST test(75.0% vs 72.2%),a positive predictive value of AFP + mSEPT9 test was higher than that of the AFP + mSST test(79.4% vs. 66.7%).In conclusions, methylated SEPT9 was a better companion marker of AFP for HCC screening than methylated SST.