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This study assessed the apical transportation using Mani GPR or HyFlex NT during the retreatment of curved root canals. Thirty‐eight roots were analysed using micro‐CT for the comparison of apical transportation produced by two retreatment systems. Longitudinal transportation, horizontal transportation, variation in the canal angle of curvature and variation in the canal/root width ratio were analysed. Longitudinal transportation was frequently observed, regardless of the system used. The canals retreated with Mani GPR showed a significantly higher horizontal transportation at 1 mm from the root apex (P < 0.01) and greater variation of the canal curvature angle (P < 0.01). The canal/root width ratio was similar between groups (P > 0.05). In conclusion, longitudinal transportation occurred more frequently in the mesial canal walls. Mani GPR showed greater horizontal transportation at 1 mm short of the apex, and higher variation of the canal curvature angle compared with HyFlex NT. [ABSTRACT FROM AUTHOR]