Nanoscale structural features of amorphous zircon and pyrochlore produced by self-irradiation induced amorphization have been characterized by small-angle X-ray scattering (SAXS). Electron density fluctuations were observed in the untreated samples and studied as a function of annealing temperature (up to 1300 °C). In untreated zircon, density fluctuations were found to have a characteristic length-scale of approximately 1 nanometer diameter. A clear scattering maximum develops at ∼3 nm–1 as a function of the degree of damage, but only for amorphous fractions higher than 70%. For the untreated pyrochlore sample such a strong signal was not observed in the scattering function. As annealing temperature increases, phase segregation is observed in zircon with a clear nucleation at 850 °C of zirconia grains. The SAXS contribution, however, points towards a lower nucleation temperature, ca. 700 °C. In the pyrochlore structure, at temperatures as low as 300 °C the appearance of a first crystalline phase, Ca2Nb2O7, is observed, with the subsequent crystallization of TiO2 at 800 °C. Observed electron density variations are compared between the two structures and discussed in terms of nanoscale phase segregation phenomena.