Separated 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 (mu-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 (R) mu-CT device after 1-week at 37 degrees 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 mm(3)) compared to CLC (0.15 +/- 0.16 mm(3)) and TI (0.18 +/- 0.24 mm(3)) (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.