To investigate the role of integrin beta 3 in invasive features of ovarian cancer SKOV3 cells, by comparing different metastatic subclones. In the present study, two cell subclones, termed as S1 and S21, which possessed high and low metastatic potential, respectively, were isolated and established from human ovarian cancer parental cell line SKOV3 by the limited dilution method. The expressions of integrin alpha v, integrin alpha v beta 3, integrin beta 3, E-cadherin, FAK and ILK in the two cell subclones were compared by means of real-time RT-PCR or flow cytometry. Subsequently, S21 was transfected with siRNA for integrin beta 3 and the effects of transfection were examined by methyl thiazolyl tetrazolium (MTT) assay, colony formation assay, Matrigel invasion assay and cell migration assay. The expressions of integrin alpha v beta 3, integrin beta 3 and E-cadherin were markedly down-regulated in S1; however, there were no significant differences in the expressions of integrin alpha v, FAK and ILK beta. Of note, more than 70% knockdown of integrin beta 3 expression was obtained by siRNA technique. The integrin beta 3-siRNA-transfected cells showed significant increases in cell proliferation, cell migration and invasive activity in contrast with the mock-transfected cells. The expressions of integrin alpha v beta 3 and E-cadherin were lower in the integrin beta 3-siRNA-transfected cells compared to the mock control. Integrin beta 3, like E-cadherin, may be also a suppressor gene down-regulating invasive features of ovarian cancer cells in SKOV3 cell subclones.