© 2020 Wiley Periodicals LLCSeparated root canal instruments may affect the quality of root canal obturation and hence the survival of endodontically treated teeth. Obturation techniques may influence filling-quality. The aim was to evaluate the obturation quality of teeth filled with different obturation techniques in the presence of apically separated instruments using micro-computed tomography (μ-CT). Notched ProTaper F2 rotary-files were separated in the apical third of 36-human mandibular incisors with single root/canal and mature apex. Samples were filled by an endodontist according to one of the following obturation techniques (n = 12): cold lateral-compaction (CLC), single-cone (SC) and thermoplastic injection (TI). Samples were scanned by the Skyscan 1,274® μ-CT device after 1-week at 37°C in 100% humidity. Images of the sections were evaluated with CTan software in terms of total-volume and volume percentage of the filling materials and voids between coronal end of the separated instrument and gutta-percha/sealer filled void-free sections. Data was analyzed using Kruskal-Wallis and Mann Whitney-U tests with a significance level of 5%. Kruskal–Wallis revealed differences among groups (p < 0.05).Pairwise comparisons revealed that less volume of voids were measured in SC (0.02 ± 0.03 mm3) compared to CLC (0.15 ± 0.16 mm3) and TI (0.18 ± 0.24 mm3) (p < 0.05); while TI was statistically similar with CLC (p > 0.05). Percentages of volumes of voids and filling materials were as follows for SC, CLC and TI, respectively: 8.88 ± 18.52% and 24.45 ± 38.40%, 46.92 ± 33.53% and 53.07 ± 33.53%, 40.54 ± 33.85% and 42.79 ± 34.45%. The obturation technique may have a significant impact on the volume of voids in the presence of a separated file. No obturation technique produced a void-free root canal filling.