In this study, the structural properties of luminescent porous silicon layers have been investigated. Double x-ray and electron diffraction patterns combined with high resolution electron microscopy (HREM) show a good agreement in that the distortion of the lattice planes in porous silicon is related to the smallness of the crystallites constituting the layers. HREM results indicate that a two-level microstructure is present in porous silicon layers. This structure consists of a crystalline part (nanocrystals) and an amorphous part (a sponge-like structure). The morphology of both parts show differences for samples grown under different conditions. A model based on this two-level microstructure is used to account for these observations. It turns out that this microstructure cannot be characterized, as often attempted, by only the measured values of the porosity and the surface area. Finally, double x-ray diffraction on post-treated porous silicon layers confirms that hydrogen desorption and readsorption or further oxidation and/or reconstruction of the oxide layer in porous silicon induce further distortion of the lattice planes.