INTRODUCTION: EndoSequence and Vortex are 2 recently developed rotary file systems that are made with traditional nickel-titanium (NiTi) and M-Wire technology, respectively. Previous studies have demonstrated better fatigue resistance of M-Wire rotary files compared with the conventional NiTi file. However, no study has compared the effects of M-Wire and conventional NiTi on transportation and centering ability. Hence, the aim of this study was to evaluate the transportation and centering ability of EndoSequence and Vortex files in mesial roots of mandibular molars by using micro-computed tomography imaging. METHODS: Sixteen extracted mandibular molars with mesiobuccal and mesiolingual canals with separate foramina were used. Preinstrumentation scans of all teeth were taken, and the teeth were divided into 2 groups. In group 1, the mesiobuccal canals were instrumented with Vortex files and the mesiolingual canals with EndoSequence files. In group 2, the mesiobuccal canals were instrumented with EndoSequence files and the mesiolingual canals with Vortex files. Two file sizes were compared, 30/.04 and 40/.04. Postinstrumentation scans were performed, and the 2 scans were compared to determine centering ability and transportation. RESULTS: The amount of transportation at 1, 3, and 5 mm was similar for both file types in both file sizes. Transportation toward the furcation area at 7 mm was greater with the 30/.04 Endosequence files compared with the Vortex 30/.04 files (P <.05), but there was no difference in size 40/.04 files. CONCLUSIONS: Overall, our study does not support the use of one rotary file system over the other (Vortex or EndoSequence) when comparing transportation and centering ability.