Point defects in crystalline SiO2, created by 2.5 MeV electron irradiation at dose below the amorphization threshold or by fast neutrons, were compared by luminescence spectroscopy. Oxygen dangling bonds (“non-bridging oxygen hole centers”, NBOHCs), peculiar to amorphous state of SiO2, were detected for the first time in electron-irradiated non-amorphized α-quartz crystal. Their presence may signal the formation of nucleation centers in crystal structure as the first step to radiation-induced amorphization. Compared to crystal, irradiated by 1019 cm−2 fast neutrons, their concentration was over 100 times lower, and their inhomogeneous broadening was at least 2.5 times smaller. Divalent silicons (“silicon oxygen deficiency centers”, SiODC(II)), inherent to oxygen-deficient or irradiated SiO2 glass, were detected in neutron-irradiated (1019 n/cm2) α-quartz but were not found after the electron irradiation. Radiation-induced interstitial O2 molecules, characteristic to irradiated glassy SiO2 and other oxide glasses, are found in α-quartz only after neutron irradiation. The oxygen atoms, displaced by the 2.5 MeV e− irradiation of α-quartz for fluences up to 1019 e−/cm2 evidently stays entirely in the peroxy linkage (Si-O-O-Si bond) form.