Objective: Since the development of nickel titanium (NiTi) rotary files a number of file systems have been developed, including ProTaper continuous rotary files and the recently developed WaveOne reciprocating files. Previous studies have demonstrated better fatigue resistance of the WaveOne file compared to the ProTaper file. However, no study has compared the effects of reciprocation and continuous rotary motion on transportation and centering ability. Hence, the aim of this study was to compare the two file systems in their transportation and centering ability in mesial roots of mandibular molars using microCT imaging. Method and Materials: Twenty seven extracted mandibular molars with mesiobuccal and mesiolingual canals with separate foramina were used. Pre-instrumentation scans of all teeth were taken, canal curvatures were calculated, and the teeth were randomly divided into two groups. In group 1, the mesiobuccal canals were instrumented with ProTaper files and the mesiolingual canals with WaveOne files. In group 2, the mesiobuccal canals were instrumented with WaveOne files and the mesiolingual canals with ProTaper files. Post-instrumentation scans were performed and the two scans were compared to determine centering ability and transportation at 1, 3, 5, and 7 mm from the apical foramen. Results: Although the WaveOne appeared to stay slightly more centered at the 1, 3, and 5 mm levels and ProTaper showed less transportation at the 1 and 3 mm levels, these differences were not statistically significant. Conclusion: Overall, this study does not support the use of one file system over the other (ProTaper or WaveOne) when comparing transportation and centering ability. Both file systems proved safe for endodontic instrumentation. Keywords: centering ability, microCT, ProTaper, transportation, WaveOne