Abstract: Objective To explore the effect of siRNA targeting Runx3 on proliferation, apoptosis, and invasive ability of HepG2 cells. Methods The Runx3-siRNA was transfected into HepG2 cells. HepG2 cells were divided into four groups: control group, liposomes group, NC-siRNA group and Runx3-siRNA group. The expression levels of Runx3 mRNA and Runx3 protein were examined by RT-PCR and Western blotting. MTT assay, flow cytometry and Transwell chamber were used to determine the effect of Runx3 on HepG2 cells proliferation, apoptosis and migration. Results MTT assay showed that the proliferation of HepG2 cells was obviously inhibited by Runx3-siRNA. The result of flow cytometry demonstrated that the apoptosis of HepG2 cells was promoted by Runx3-siRNA. The invasion of HepG2 cells was also significantly inhibited by Runx3-siRNA according to Transwell chamber assay. Conclusions Silence Runx3 could effectively inhibit cell proliferation and migration, and promote apoptosis in HepG2 cells. Our study shows that Runx3 gene plays an important role on the occurrence and development in hepatocellular carcinoma. Runx3 could be a new target for the treatment of hepatocellular carcinoma.