Self-aligned nanostructures (SAN) made by reacting Co nanoparticles with crystalline Si substrates at high temperatures were studied with grazing incidence X-ray absorption spectroscopy (GI-XAS). The results from extended X-ray absorption fine structure (EXAFS) analysis and X-ray absorption near-edge spectroscopy (XANES) were used to identify SAN as crystalline CoSi2. Theoretical calculations of EXAFS and XANES spectra of several crystalline cobalt silicides were performed with the FEFF8 package. On the basis of these studies, the SAN samples were determined to contain nearly pure CoSi2.