We developed the epitaxial growth technique of various kinds of nanodots (NDs) on Si substrates using ultrathin SiO 2 film. Fe-based NDs were epitaxially grown on Si substrates without intermixing with Si atoms in Si substrates despite the easy reaction of Si and Fe, resulting in atomically sharp interfaces between NDs and substrates. The status control of the nuclei was important at the nucleation stage in terms of control of ND crystal structure. The proper nuclei also suppressed the undesirable reactions such as intermixing of Fe and Si in Si substrates. The epitaxial NDs formed by our technique can supply the prospect for the application to some devices.