The purpose of this study was to evaluate and compare the effect of Reciproc Blue (RPCB), XP-endo Shaper (XPS), and WaveOne Gold (WOG) single-files on dentinal microcrack formation using micro-computed tomography (micro-CT). Twenty-four mesial roots (24 mesio-buccal and 24 mesio-lingual canals) of mandibular molar teeth were prepared using RPCB, XPS, and WOG files (n = 8/each group). The samples were scanned with micro-CT in the pre- and post-preparation. Then, before preparation and after preparation cross-sectional images of the teeth were evaluated to detect the presence of microcracks. For each group, the number of microcracks was calculated as a percentage rate. The data were statistically analyzed using McNemar at 5% significance level (p < .05). Dentinal microcracks were observed in 25.99% (2,103 of 7,813), 31.99% (2,482 of 7,758), and 36.66% (2,836 of 7,731) of cross-sectional images of the XPS, WOG, and RPCB groups, respectively. In all the groups, all the dentinal microcracks seen in the post-treatment cross-sectional images were present in the corresponding pre-treatment images. Within the limitations of this study, the XPS, WOG, and RPCB files did not cause new dentinal microcrack formation or propagation of existing dentinal microcracks.