While several materials and techniques have been used to assess the quality of root canal fillings in micro-CT images, the lack of standardization in scanning protocols has produced conflicting results. Hence, the aim of this study was to determine a cutoff voxel size value for the assessment of root canal filling voids in micro-CT and nano-CT images. Twenty freshly extracted mandibular central incisors were used. Root canals were prepared with nickel titanium files to an ISO size 40/0.06 taper and then filled with a single cone (40/0.06 taper) and AH Plus sealer. The teeth were scanned with different voxel sizes with either micro-CT (5.2, 8.1, 11.2, and 16.73 mu m) or nano-CT 1.5 and 5.0 mu m) equipment. Images were reconstructed and analyzed with the NRecon and CTAn software. Void proportion and void volume were calculated for each tooth in the apical, middle, and coronal thirds of the root canal. Kruskal-Wallis and post hoc Mann-Whitney U tests were performed with a significance level of 5%. In micro-CT images, significantly different results were detected among the tested voxel sizes for void proportion and void volume, whereas no such differences were found in nano-CT images (p > 0 05). Micro-CT images showed higher void numbers over the entire root length, with statistically significant differences between the voxel size of 16.73 mu m and the other sizes (p < 0 05). The values of the different nano-CT voxel sizes did not significantly differ from those of the micro-CT (5.2, 8.1, and 11.2 mu m), except for the voxel size of 16.73 mu m (p < 0 05). All tested voxel sizes enabled the detection of root canal filling voids except for the voxel size of 16.73 mu m. Bearing in mind the limitations of this study, it seems that a voxel size of 11.2 mu m can be used as a reliable cutoff value for the assessment of root canal filling voids in micro-CT imaging.