The aims of this study were to evaluate the quality of canal filling using mineral trioxide aggregate (MTA) and gutta-percha (GP) in root canals, and to investigate the differences in the percentage of voids between mesial and distal canals by using microcomputed tomography. Twenty-two extracted human mandibular molars were instrumented using rotary files. Two teeth without canal fillings served as negative controls, and the other teeth were obturated with either ProRoot ® MTA or gutta-percha and AH Plus ® sealer. Obturated teeth were scanned with microcomputed tomography, and the percentage of voids (V %) was calculated. These specimens were also examined under a scanning electron microscope. The MTA group showed a significantly higher V % than the GP groups (p<0.05). The mesial canal groups showed significantly higher V% than did the distal canal groups (p<0.05). In orthograde filling, MTA exhibited significantly lower filling quality than did GP.