The influence of fast neutron irradiation on the structure and spatial distribution of Ge nanocrystals (NC) embedded in an amorphous SiO2 matrix has been studied. The investigation was conducted by means of laser Raman Scattering (RS), High Resolution Transmission Electron Microscopy (HR-TEM) and X-ray photoelectron spectroscopy (XPS). The irradiation of Ge- NC samples by a high dose of fast neutrons lead to a partial destruction of the nanocrystals. Full reconstruction of crystallinity was achieved after annealing the radiation damage at 8000C, which resulted in full restoration of the RS spectrum. HR-TEM images show, however, that the spatial distributions of Ge-NC changed as a result of irradiation and annealing. A sharp decrease in NC distribution towards the SiO2 surface has been observed. This was accompanied by XPS detection of Ge oxides and elemental Ge within both the surface and subsurface region.