Background: Smear layer is always formed during the instrumentation process due to the action of endodontic instruments during the shaping process and it should be removed as it might decrease the overall success of endodontic therapy. Aim of the study: To compare the cleaning efficiency of different rotary Ni-Ti systems: ProTaper Next, Xpendo Shaper and WaveOne Gold by assessing their ability to remove the smear layer from root canals walls. Methods and materials: A total of 24 palatal roots of maxillary molars were used in this study and randomly assigned into 3 groups (n=8) as follows: Group 1: instrumentation with ProTaper Next system (Dentsply Maillefer, Switzerland), Group 2: instrumentation with Xp-endo Shaper system (FKG Dentaire, Switzerland) and Group 3: instrumentation with WaveOne Gold system (Dentsply Maillefer, Switzerland). The samples were irrigated with 5.25% NaOCl. All samples were then examined by scanning electron microscope (SEM) at the center of the coronal, middle and apical thirds. The data was statistically analyzed using Kruskal Wallis and Mann-Whitney U tests. Results: ProTaper Next files showed a lower average mean of smear layer when compared to WaveOne Gold and Xp-endo Shaper files at the coronal third. No significant differences between the average means of smear layer were found at the middle and apical thirds. Conclusion: None of the tested groups showed a completely smear layer free root canal walls. In general, ProTaper Next files showed the best performance at the coronal third. All the files showed comparable performance at the middle and apical thirds.