Background: Root canal preparation during endodontic treatment may be associated with various complications, including a change in the original pathway of the root canal lumen. The aim of our study was to determine whether files of similar sizes that use various movement kinematics (rotary, reciprocal, adaptive motion) cause root canal transportation, and whether the differences between such systems are statistically significant. Methods: The degree of root canal transportation (DT) was calculated with the use of computed tomography scans for 3 groups of teeth (for each group: n = 20) in which the root canals were prepared using either rotary (ProTaper Next—PTN), reciprocal (WaveOne Gold—WOG), or adaptive movement (Twisted Files—TF) instruments. Results: For rotary ProTaper Next instruments, the mean value of the DT index was 0.0795 (SD = 0.0179) for 3 mm from the apex, 0.09 (SD = 0.0262) for 6 mm from the apex, and 0.106 (SD = 0.0221) for 9 mm from the apex. For reciprocal WaveOne Gold Primary instruments, the mean value of the DT index was 0.0355 (SD = 0.015) for 3 mm from the apex, 0.061 (SD = 0.02) for 6 mm from the apex, and 0.08 (SD = 0.25) for 9 mm from the apex. For Twisted Files, the mean value of the DT index was 0.05 (SD = 0.03) for 3 mm from the apex, 0.092 (SD = 0.17) for 6 mm from the apex, and 0.08 (SD = 0.02) for 9 mm from the apex. Conclusions: The use of PTN, WOG, and TF files resulted in root canal transportation to a different degree. The use of rotary PTN files produced the most transported preparation, whereas the use of WOG files produced the conservative root canal preparation that allowed the retention of the original shape of the root canal.