Background: During the preparation process of root canals, endodontic instruments deviate from the long axis of the canal. This study aimed to assess and compare the apical transportation induced by different reciprocating single-file systems in curved canals. These canals were obturated with GuttaCore and single-cone obturation techniques using microcomputed tomography (m-CT). Mehtods: A total of sixty-four mandibular molar teeth were selected, which have root canal systems with two independent severely curved canals in the mesial root. The root canals were first instrumented using the WaveOne Gold primary file and subsequently obturated using either the Single-cone or GuttaCore obturation techniques. Following the first m-CT scan, the samples were divided into four classes for each obturation technique (sixteen canals for every group). Next, these groups were categorized based on the retreatment system, as follows: group R) the Reciproc R25 file, group RB) the Reciproc Blue R25 file, group WO) the WaveOne primary file 25, and group WOG) the WaveOne Gold primary file 25. After the retreatment procedures, a second m-CT scan was conducted, and the apical transportation was calculated for analysis at 2, 3, and 4 mm from the apex. Results: In the Reciproc and WaveOne groups, apical transportation was significantly higher than in the Reciproc Blue and WaveOne Gold groups. Conclusion: Reciproc and WaveOne files have higher apical transportation than the Reciporc Blue and WaveOne Gold files. The lowest apical transportation occurred at 2 mm from the apex.