Silicone rubber substrates were irradiated at an acceleration voltage of 7 kV and a dose of 1×1015 ions/cm2 by the simultaneous use of oxygen cluster and monomer ion beams, and then soaked in CaCl2 solution. Apatite-forming ability of the substrates was examined using a metastable calcium phosphate solution that had 1.5 times the ion concentrations of a normal simulated body fluid (1.5SBF). After the irradiation, the silicon oxide clusters (SiOx) were formed at the silicone rubber surface. The hydrophilicity of the substrates was remarkably improved by the irradiation. The irradiated silicone rubber substrates formed apatite in 1.5SBF, whereas unirradiated ones did not form it. These results suggest that the functional groups such as Si–OH and/or COOH groups induced apatite nucleation in 1.5SBF.