Background and objectives: Root canal preparation following obturation with rotary instruments and different obturation techniques may lead to formation of microcracks in the root canal wall, void and gaps between the canal wall and obturation material. Aim: This study aimed to evaluate dentinal microcracks and voids formation after using two different files TruNatomy (TRN) and Genius (GN) and two obturation techniques Single Cone (SC) and GuttaCore (GC) using Microcomputed tomography scan (micro-CT). Methods: 40 extracted mandibular premolars were decoronated, leaving 13mm roots. The roots were randomly divided into two main groups TRN and GN ((n=20)) according to instrumentation, afterwards each group subdivided into two subgroups ((n=10)) according to obturation techniques. The root canals instrumented with TRN and GN file and obturated with Single Cone (SC) and GuttaCore (GC) obturation techniques. AH Plus sealer was used in all groups. The specimens were scanned with Micro-CT before and after root canal preparation and after obturation. subsequently, all pre-and postoperative cross-sectional images of the roots were screened to identify the presence of dentinal defects. Furthermore, the percentage of voids volume calculated. Data were analyzed statistically to determine difference between groups, the level of statistical significance was at p < 0.05. Results: GN revealed the least number of microcracks. There were no significant differences between groups in the incidence of dentinal microcracks. The highest percentage of filling material was observed in GC groups. There were significant differences between the obturation groups in the number of voids present after obturation (P < 0.001). Conclusion: The instrumentation of root canals induces dentinal microcracks. Obturation have no effect on the formation of cracks. None of the root canal filling procedures yield fillings that are void-free. Keywords: Dentinal crack, Voids, Micro CT, Guttacore, Singlecone, TruNatomy, Genius.