The aim of this investigation was to compare the cleaning and shaping efficiency of Self-adjusting file and Protaper, and to assess the correlation between root canal curvature and working time in mandibular molars using micro-computed tomography. Twenty extracted mandibular molars instrumented with Protaper and Self-adjusting file and the total working time was measured in mesial canals. The changes in canal volume, surface area and structure model index, transportation, uninstrumented area and the correlation between working-time and the curvature were analyzed. Although no statistically significant difference was observed between two systems in distal canals (p>0.05), a significantly higher amount of removed dentin volume and lower uninstrumented area were provided by Protaper in mesial canals (p<0.0001). A correlation between working-time and the canal-curvature was also observed in mesial canals for both groups (SAFr 2 =0.792, p<0.0004, PTUr 2 =0.9098, p<0.0001)