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The structure of amorphous and crystalline SiGe nanoparticles, embedded in a dielectric medium, SiO2, and its stability under 'in situ' electron beam irradiation is reported. High-resolution transmission electron microscopy and electron-diffraction pattern simulation by fast Fourier transform was used to analyze the crystal structure of the SiGe nanoparticles. Electron beam irradiation induces structural alternate order-disorder transitions in the nanoparticles for irradiation effects are mainly associated to the density of current. For irradiation with current densities < 7 A.cm--2 no effects are observed in the as-deposited amorphous samples, whereas in the crystallized samples, SiGe nanocrystals show higher stability and no effects are observed for irradiation densities of current < 50 A-cm-2. Irradiation with densities of current greater than these thresholds cause consecutive amorphous-crystalline or crystalline-amorphous structure transitions respectively for both amorphous and crystallized nanoparticles. A hexagonal structure is proposed for those nanocrystals obtained after irradiation in the as deposited amorphous samples.