Fourier transformed infrared spectroscopy (FTIR) has been employed to observe and understand structural variations in SiO2 matrix during the formation of Ge and Si nanocrystals by ion implantation as a function of processing parameters. The Si-O asymmetric stretching peak of absorption spectra were used to monitor the evolution of SiOx (x < 2) films during the annealing process. It was shown that the recovery process in Si-O network is quite different in Ge and Si implanted samples and the deformation caused by Ge atoms in the SiO2 matrix can be recovered by annealing the implanted samples at lower temperatures than that by Si atoms. This is in agreement with the formation kinetics of the Si and Ge nanocrystals in SiO2 as observed by Raman spectroscopy and photoluminescence measurements of the same samples. (c) 2005 Elsevier B.V. All rights reserved.