The aim of the present micro-computed tomography (Micro-CT) analysis was to compare the quality of obturation in the apical third of the root with the warm vertical compaction (WVC) and single matching taper sized cone (SMTSC) techniques. Mesial roots of 16 freshly extracted mandibular first molar teeth (with a total of 32 canals) were used. Canals in each mesial root were shaped to a size F3 Protaper and were randomly assigned to either continuous wave vertical compaction or single match tapered size cone technique. Volume of voids and gaps in the obturated roots were measured using micro-CT scanning at 1, 3, and 5 mm from the apex of the root. There was no statistically significant difference in the volume of voids measured at 1 mm (p > 0.05), 3 mm (p > 0.05) and 5 mm (p > 0.05) filled with either WVC and SMTSC techniques. The quality of obturation in the apical third of the root with the WVC and SMTSC techniques is comparable. SCANNING 38:352–356, 2016.