Self-organized transition-metal (Ni and Fe) and rare-earth (Er) silicide nanostructures were grown on Si(111) and Si(001) surfaces under low coverage conditions, in a “solid phase” and “reactive deposition” epitaxial regimes. Island evolution was continuously monitored in-situ, using real-time scanning tunneling microscopy and surface electron diffraction. After anneal of a Ni/Si(111) surface at 700°C, we observed small hemispherical Ni-silicide nanoislands ∼10nm in diameter decorating surface steps in a self-ordered fashion and pinning them. Fe-silicide nanoislands formed after a 550°C anneal of a Fe-covered surface, were also self-ordered along the surface step-bunches, however were significantly larger (∼70×10nm) and exhibited well-developed three-dimensional polyhedral shapes. Ni-silicide islands were sparsely distributed, separated by about ∼100nm from one another, on average, whereas Fe-silicide islands were more densely packed, with only ∼50nm mean separation distance. In spite of the above differences between both types of island in size, shape, and number density, the self-ordering in both cases was close to ideal, with practically no islands nucleated on terraces. Superconducting quantum interference device magnetometry showed considerable superparamagnetism, in particular in Fe-silicide islands with ∼1.9μB/Fe atom, indicating stronger ferromagnetic coupling of individual magnetic moments, contrary to Ni-silicide islands with the calculated moments of only∼0.5μB/Ni atom. To elucidate the effects of the island size, shape, and lateral ordering on the measured magnetic response, we have controllably changed the island morphology by varying deposition methods and conditions and even using differently oriented Si substrates. We have also begun experimenting with rare-earth silicide islands. In the forthcoming experiments we intend to compare the magnetic response of these variously built and composed islands and correlate between their composition, crystal and morphological characteristics, and the resultant magnetic properties.