Aim: This study was designed to evaluate the influence of pre-flaring on the apical transportation and dentinal damage after preparation of curved root canals using EndoStar (ES5), OneShape (OS) and ProTaper Next (PTN) systems. Material and Methods: Hundred and twenty human mandibular first molars were selected. Pre-operative imaging by CBCT was done for measurement of apical transportation of mesio-buccal root canals then saved. The specimens were grouped into: Group I: Instrumented by ES5 files; Group II: by OS single file; and Group III: by PTN files. Each group was subdivided into subgroups: A: Instrumented without pre-flaring; and B: pre-flared before instrumentation. After instrumentation, all specimens were scanned under the same way as the pre-operative scan and data were saved on the software for evaluation of apical transportation. Roots were sectioned perpendicular to long axis at 3, 6 and 9mm from the apex and viewed under SEM for detection of any defect arise from lumen outwards. The significance was set at P < 0.05. Results: All values of apical transportation at level 2mm from apex were positive that indicated direction of transportation toward mesial direction of root canal, whereas at level 4mm from apex were negative that indicated direction of transportation toward distal direction of root canal. In dentinal defects at 6 mm, the higher percent of cracks was noted in OS and the lowest for PTN. Conclusions: Pre-flaring of root canal reduces the apical transportation and dentinal defects when curved root canals were prepared with Ni-Ti instruments.