In this letter, we show that self-assembled α- FeSi2 nanorods could be formed at the Si(100) surface by the ion beam implantation method. The microstructures and basic crystallographic relationships between the silicide nanocrystals and silicon substrate were investigated using transmission electron microscopy (TEM), and the experimental results revealed the growth mechanism of the nanorods. Our results indicated that the anisotropy in interfacial energy is the main cause for the nanorod formation.