<p><strong>Background:</strong> Root canal preparations done using many rotary endodontic instruments results in formation of root dentin defects because of the stress induced by the instruments within the root canal during cleaning and shaping, thereby worsening the long term prognosis of the root canal treated teeth. Many rotary instruments are been globally studied for the purpose of generating a correct instrument for root canal preparation.</p><p><strong>Objective:</strong> This study was done to evaluate the effect of HyFlex EDM, which is a new rotary system on root dentin during root canal preparation.</p><p><strong>Materials and methods:</strong> Fourteen single rooted premolars were selected and divided into two groups, Group 1-Protaper Universal and Group 2-HyFlex EDM. All the specimens were decoronated. Roots of each specimen were sectioned at 3mm, 6mm and 9mm and were then viewed under stereomicroscope for dentinal defects. t-test was done for the statistical analysis and level of significance was set at p=0.05.</p><p><strong>Results:</strong> Protaper Universal showed highest percentage of defect than HyFlex EDM.</p><p><strong>Conclusion:</strong> HyFlex EDM showed lowest percentage of defects in root dentin. Thus, HyFlex EDM is more efficient in root canal preparation than that of Protaper Universal thereby preventing dentinal defects or microcracks leading to root fractures.</p>