We report the structural changes inside germania glass induced by femtosecond laser pulses. Inspection by polarization microscopy and secondary electron microscopy indicate that the periodic nanostructures consist of oxygen defects such as ODCs (oxygen deficient centers) and NBOHCs (nonbridging oxygen hole centers) for laser pulse energy less than 0.2 mu J. However, the glass network was dissociated and O-2 molecules were generated for laser pulse energy greater than 0.4 lJ. Two different structural changes, form-birefringence and dissociation, were induced in GeO2 glass, depending on the laser pulse energy. The form-birefringence exhibited by the nanogratings in GeO2 glass is larger than that in SiO2 glass for pulse energy less than 0.2 mu J, as the density of nanovoids enclosed by ODCs in GeO2 glass is higher than that in SiO2 glass. Arrhenius plots of the phase retardation caused by the nanogratings in GeO2 and SiO2 indicate that the oxygen defects are relaxed at a temperature 100 degrees C above the glass-transition temperature.