Thirty specimens were scanned in micro-CT and divided into three groups according to the instrumentation type: pediatric motor-driven Sequence baby File (SBF); conventional motor-driven (Sequence Rotary File - SRF); manual K file. Instrumentation time was timed. After preparation, the specimens were scanned again. The pre- and post-instrumentation images were superimposed to measure the amount of root canal deviation and the resin remnant thickness. ANOVA followed by the Tukey test analyzed the comparisons between groups (p<0.05). No statistically significant differences occurred in root canal deviation among groups (p>0.05). There were statistically significant differences in the comparison among root thirds (p<0.001) but without significant differences in the interaction group vs. root third (p>0.05). Both motor-driven instrumentations showed statistically greater weariness than manual instrumentation (p<0.001), without significant significant differences between SBF and SRF. Motor-driven instrumentation had a shorter working time than manual instrumentation (p<0.001). Pediatric motor-driven instrumentation demonstrated good outcomes in relation to root canal deviation and amount of remnant structure, with shorter instrumentation time. SBF can be a suitable alternative for endodontic instrumentation in primary molars.
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