© 2021 BSPD, IAPD and John Wiley & Sons LtdBackground: Although single-file rotary systems are accepted in the field of paediatric dentistry in terms of providing time advantage, research works continue due to the variable anatomical structure of the root canal. Aim: This study aimed to evaluate rotary systems in different kinematics in terms of microcracks and the shaping of the danger zone in primary molars by micro-CT. Design: The mesial canals of primary molars (n = 30) were used. Root canals in each group (n = 10) were prepared with single-file rotary systems (One Shape®, OS; XP-endo® Shaper, XP-ES; WaveOne Gold, WOG). The images were evaluated for dentin thickness in the danger zone and microcrack formation. Results: WOG caused the highest dentin reduction in the danger zone area. OS led to significantly less dentin reduction than XP-ES and WOG (P <.05). The XP-ES showed the highest number of microcracks (P <.05). No statistically significant difference was found between WOG and OS (P >.05). In all systems, more microcracks were observed in the middle third than coronal and apical. Conclusion: Within the limitations of this study, the rotary systems were superior to reciprocating in terms of shaping ability in the danger zone. It is thought that further studies with different systems should be designed considering the anatomical variations and chemical composition of primary teeth.