To assess the root canal system morphology of mandibular molars by means of micro-computed tomography, one hundred and four mandibular first molars were investigated and the following were evaluated: Vertucci's classification, the presence of lateral canals and the number of apical foramina. Mesial root canal surface area and volume were obtained by the CTAn and CTvol software. The type of root canal isthmi was classified applying the Hsu & Kim and Fan criteria. The most frequent root canal configuration was Vertucci type IV (46.2%). Lateral canals were observed in all root canal thirds and the average number of apical foramina was 3.15 ± 1.77. Regarding the presence of isthmus, Types I and II were the most prevalent, according to Hsu & Kim and Fan et al. criteria, respectively. Mesial root canals of mandibular molars showed high morphology variability.