The epitaxial relationships in buried FeSi2 layers prepared by ion beam synthesis at elevated temperatures in both (111) and (100) silicon substrates are investigated by means of conventional and high-resolution transmission electron microscopy and electron diffraction in as-implanted and annealed samples. Except for two epitaxial relationships between the beta-FeSi2 grains and the silicon previously reported for other preparation techniques, a new relationship is also identified. Misfit dislocations are observed on the silicide/silicon interface and slacking faults in the grains. In as-implanted samples and in material annealed at 1150 degrees C, alpha-FeSi2 occurs both aligned and twinned with respect to the silicon substrate.