Reciprocating instruments made from M-wire alloy have been proposed to reduce the risk of fracture. No information is available on the surface alteration after single and multiple uses in root canals. Two reciprocating NiTi instruments were used on extracted teeth up to three times. ESEM/EDS analysis was conducted to determine defects, alterations, and wear features of the apical third of instruments and metallographic analysis was performed on the cross-section of new and used instruments to compare alloy properties. Topography of apical portion was evaluated by AFM before and after uses. Extracted single-rooted teeth were divided into two groups and instrumented according to the manufacturer's recommendations with: (A) WaveOne Primary and (B) Reciproc R25. Each group was divided into three subgroups according to the number of canals instrumented: 1, 2, and 3, respectively. Chi square test was performed to verify homogeneity of defects distribution and GLM to evaluate the differences of RMS at baseline and after use for both groups (α level 0.05). No instrument fractured and no spiral distortions were observed under optical microscope even when the number of uses increased. Not significant differences were found for WaveOne and Reciproc. Blades presented a wrapped portion in WaveOne group and a more symmetrical feature in Reciproc group. Metallographic analysis revealed in both groups the presence of twinned martensitic grains with isolated flat austenitic areas. Both instruments demonstrated limited alteration, such as tip deformation and wear. This study confirmed the safe clinical use of both instruments for shaping multi-rooted teeth. SCANNING 36:517–525, 2014. © 2014 Wiley Periodicals, Inc.