Magnetic and electrical properties of the nanostructured ZnO films are affected by the nonrandom distribution of impurities in the film due to segregation at grain boundaries (GBs) or extended defects. However, mapping the nature and distribution of the impurities in the film is not trivial. Here we demonstrate a simple, statistically relevant, and nondestructive procedure of quantitative determination of the paramagnetic impurities segregated at the GBs in nanostructured semiconducting and insulating films. From correlated electron paramagnetic resonance and transmission electron microscopy investigations, we determined the localization of trace amounts of Mn(2+) ions, present as native impurities in a ZnO film deposited by magnetron sputtering at room temperature. In the as-deposited ZnO film, the Mn(2+) ions were all localized in nanosized pockets of highly disordered ZnO dispersed between nanocrystalline columns. After the samples had been annealed in air at >400 °C, the size of the intercrystalline region decreased and the diffusion in GBs was activated, resulting in the localization of a portion of the Mn(2+) ions in the peripheral atomic layers of the ZnO columns neighboring the GBs. The proportion of Mn(2+) ions still localized at the GBs after annealing at 600 °C was 37%. The proposed method for the assessment of the presence and nature of impurities and the quantitative evaluation of their distribution in semiconducting and insulating nanostructures is expected to find direct applications in nanotechnology, in the synthesis and quality assurance of thin films for spintronics and opto- and nanoelectronics.