Purpose: This study was directed to evaluate the cleaning effectiveness& the dentinal defects incidence after preparation with different Ni-Ti rotary instruments in permanent molar root canals. Materials and Methods: A 60 human permanent lower first molars were used in this study. According to the Ni-Ti rotary system used in canal instrumentation, specimens were divided into 3 main groups (n=20) (One Shape, HyFlex EDM and XP-Endo Shaper). Each system was used as the suggested settings by manufacture. Each group was received Copious irrigation with 2.6% NaOCl was performed after the use of each file and finally with combination of 17% EDTA and 2.6% NaOCl. Then specimens were washed with distilled water. Each main group was divided into two subgroups (A &B) (n=10) according to evaluation methods: Subgroup A: The cleaning effectiveness (Scanning electron microscopic (SEM) evaluation). Subgroup B: The incidence of dentinal defects (Steriomicroscope evaluation). Results: Regarding to cleaning effectiveness, highest mean and standard deviation values were recorded for HF system while lowest mean value was recorded for XP system. Regarding to dentinal defects, the highest mean and standard deviation values were recorded for OS system, while the lowest mean value was recorded for XP system. Conclusions: The results of the present study showing that: XP-Endo Shaper file gives promising better results in cleaning ability with minimal incidence of dentinal defects found in root dentin.