The purpose of this in vitro study was to evaluate the shaping ability of reciprocating and continuous rotary systems after root canal retreatment. After preparation and root canal filling, mesial canals of 54 mandibular molars were distributed into 3 groups (n=18), according to the filling material removal and re-instrumentation protocols: WOG group - WaveOne Gold system; PTN group - ProTaper Next system; and PTU group - ProTaper Universal system. Cone-beam computed tomographic (CBCT) images acquisition of the mesial root canals was performed at different moments: (1) before instrumentation (unprepared root canals), (2) after preparation and filling, (3) after filling material removal and (4) re-instrumentation. The apical transportation (AT), centering ability (CA) and change in root canal diameter were assessed by CBCT analysis. The remaining filling material quantification was performed by radiographic examination. The statistical analyses were performed using the 3-way ANOVA, Tukey-Kramer, Kruskal-Wallis and Dunn multiple Comparison tests (p<0.05). The tested instruments did not show full CA (=1.0). PTN group had greater AT at the 5th mm in comparison with the WOG group (p<0.05). After re-instrumentation, WOG group had greater root canal diameter change at the 1st and 5th mm than PTN and PTU groups (p<0.05). There was no significant difference among groups when comparing the amount of remaining filling material after re-instrumentation (p>0.05). The tested systems provided minimal alteration in root canal morphology at the apical portion after root canal retreatment. However, WOG promoted greater change in root canal diameter.