Objective <p>We evaluated the effect of brushing motion on microcrack formation in round distal canals after using multi-file rotary(MFR), single-file rotary(SFR), and single-file reciprocation(SFRc) systems via micro-computed tomography(micro-CT).</p> Materials and methods <p>Thirty-six mandibular molars were used. Samples were allocated according to files and preparation patterns (<i>n</i> = 12); pecking (P) and brushing (B): Group-MFR-P, Group-MFR-B, Group-SFRc-P, Group-SFRc-B, Group-SFR-P, Group-SFR-B. MFR was ProTaper Next, SFR was TruNatomy, and SFRc was WaveOne Gold. Mesial and distal were prepared using pecking motion, and additional brushing motion. Brushing motions were performed after the pecking motions with 6 strokes. Pre-and-post-instrumentation scans were obtained. Wilcoxon, Krukal-Wallis, and Mann-Whitney-U were performed.</p> Results <p>No differences were between pre-and-post-instrumentation scans (<i>p</i> &gt; 0.05). Post-instrumentation microcracks were not different in Group MFR-P and Group MFR-B, Group SFRc-P and Group SFRc-B, Group SFR-P and Group SFR-B (<i>p</i> &gt; 0.05).</p> Conclusion <p>The brushing motion followed by the pecking motion did not cause microcracks. None of the file systems examined in the study induced microcracks.</p>