This work reports on the structural characterization of Au nanocrystals directly prepared on the surface of (100)Si and 150 nm-thick SiO2 deposited (100)Si substrates, by a physical self-assembly method, consisting in the UHV evaporation of a thin Au film and its successive high temperature annealing. The morphology, orientation, and crystalline structure of Au nanocrystals were characterized by scanning and high-resolution transmission electron microscopy and X-ray diffraction, respectively. Experimental results show that the nature of the substrate strongly influences the process of Au nanocrystal formation upon heat treatment, by affecting the interaction of deposited Au with the underlying material. In the case of clean (100)Si substrates the Au strongly interacts with Si, so that Au nanoislands are obtained with a well defined epitaxial relationships with the substrate, i.e. [100]AuÐÐ[110]Si and [110]AuÐÐ[311]Si. The nanoisland shape is affected by faceting at the Au/Si interface, the Au nanocrystal being limited by the {111}, {311}, {711} and {-111} planes of Si. In the case of SiO2/(100)Si substrates spherical shaped Au nanoparticles with random crystal orientation are instead, produced.