MSH3-rs33002 (TT), MSH3-rs26779 (TT), MSH3-rs32950 (GG) were more likely to increase HCC risk (P=0.038, OR=1.746; P=0.045, OR=1.603 and P=0.001, OR=1.943). Here, MSH3 is linked to hepatocellular carcinoma.