We investigated zircon from high-grade metagranites of the Serbo-Macedonian Massif, in Bulgaria, by cathodoluminescence (CL), back-scattered-electron imaging, electron-microprobe analysis, and Raman microspectroscopy. The structural state in various zones was assessed using: (i) the position and width of the Raman peak near 1008 cm−1, (ii) the relative Raman intensity of the symmetrical and anti-symmetrical SiO4 modes, (iii) the width of the peaks near 357 and 439 cm−1, and (iv) the occurrence of extra Raman scattering near 162, 509, 635 and 785 cm−1. The analyzed zones are divided into two main groups: (A) areas with a well-resolved Raman peak near 1008 cm−1, and (B) areas with a very weak Raman scattering near 1008 cm−1. Group B can be classified into two subgroups: (B-i) dark zones in CL images, with a high concentration of uranium (up to 7000 ppm), and (B-ii) outermost bright zones in CL images with a concentration of U lower than that in the inner areas and commonly below the detection limit. The samples from group A contain uranium at intermediate levels of concentration (~350–2000 ppm), and exhibit a linear correlation between the width and the position of the peak near 1008 cm−1. The relatively narrow width of this peak provides evidence of structural recovery due to annealing of accumulated radiation-induced damage. In zircon from equigranular metagranites, which are relatively less deformed and migmatized, three types of spatial regions are observed: the least-damaged regions with a structure altered mainly by point defects, moderately damaged regions characterized by faults with translational symmetry, and heavily damaged zircon with additional medium-range disorder involving changes in the mutual orientation of the cation–oxygen polyhedra and in their connectivity. The zircon separated from more deformed and strongly migmatized rocks is relatively homogeneous in its texture and chemical composition, and its structure consists of incipient grains of zircon.