Introduction <p>The aim of this study was to evaluate the amount of dentin removed and the incidence of dentinal microcrack formation in the “danger zone” of the mesial and distal root canals of mandibular primary molars using three different root canal instrumentation systems.</p> Methods <p>Mesial and distal root canals of mandibular primary molars (n = 66) were included in the study. The teeth were randomly assigned to three groups according to the instrumentation technique: conventional hand instrumentation, Kedo-SG, and Pro-Af Baby Gold rotary systems. Micro-Computed Tomography (Micro-CT) scans were obtained before and after root canal preparation. The amount of dentin removed from the danger zone and the presence of dentinal microcracks were evaluated using the reconstructed images.</p> Results <p>No statistically significant differences were observed among the groups in terms of the amount of dentin removed from the danger zone at either measurement level in both mesial and distal roots (p &gt; 0.05). Similarly, no statistically significant differences were found among the groups regarding dentinal microcrack formation in either root. However, a lower incidence of microcrack formation was observed in the Kedo-SG rotary file system. When evaluated according to root regions, microcracks were most frequently detected in the coronal third, followed by the middle third, and least frequently in the apical third in both roots.</p> Conclusion <p>No significant differences were observed among the instrumentation systems in terms of dentin removal from the danger zone or dentinal microcrack formation. Although the Kedo-SG group showed fewer microcracks numerically, no statistically significant difference was found. Further studies are needed to evaluate the potential clinical advantages of single-file rotary systems in primary teeth.</p>