Damaged structures in the MgAl(2)O(4)spinel induced by swift heavy ions were investigated using the X-ray absorption near edge structure (XANES) and small angle X-ray scattering (SAXS). Increasing the fluence of 100 MeV Xe ions leads to increased SAXS intensity and XANES spectral changes on both Mg and AlK-edges. The damaged regions of ion tracks were observed by SAXS to be cylindrical in shape with a diameter of 5 nm. The theoretical XANES spectra indicated that the changes in the experimental spectra were due to the cationic disordering between tetrahedral and octahedral sites. This disordering caused an increase in the inversion degree of the cations. Furthermore, the quantitative analysis of the XANES spectra revealed the preferential occupation of cations at the octahedral sites at high fluence.