Interdiffusion between Si substrate and nanorod arrays of Au, Pt, and AuPt nanoalloys is investigated at temperatures lower than the AuSi eutectic temperature. When the nanorod is pure Au, Si diffusion from the substrate is very rapid. Au atoms are completely replaced by Si, converting the nanostructure into one of Si nanorod arrays. Au is diffused out to the substrate. The Au nanorod arrays on Si are unstable. When the nanorod is pure Pt, however, no diffusion of Si into the nanorod or any silicide formation is observed. The Pt nanorods are stable on Si substrate. When the nanorods are an alloy of AuPt, interesting interactions occur. Si diffusion into the nanorods is rapid but the diffusing Si readily reacts with Pt forming PtSi while Au diffuses out to the substrate. After annealing, nanophases of Au, Pt, PtSi, and Si may be present within the nanorods. When the Pt content of the alloy is low (12 at%) all Pt atoms are converted to silicide and the extra Si atoms remain in elemental form, particularly near the tip of the nanorods. Hence, the presence of Au accelerates Si diffusion and the ensuing reaction to form PtSi, a phenomenon absents in pure Pt nanorods. When the Au content of the alloy is low, the Si diffusion would cease when all Au atoms have diffused out of the nanorod, thereby arresting the silicide formation resulting in excess Pt in elemental form within the nanorod. This is a technique of making Si nanorods with and without embedded PtSi nanophase consisting of heterojunctions which could have unique properties.