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.