The aim of this study was to assess the performance and surface alteration of two single-file systems according to the number of uses. Ten WaveOne Primary files (25/.08) and ten One Shape NG files (25/.06) were used for instrumentation of mesial root canals of mandibular molars. Each instrument was cleaned and sterilized after the preparation of two root canals and then reused. The time spent for instrumentation of each root canal was recorded and analyzed by using t-test. Microphotographs of the surface of the instruments were taken with a scanning electron microscope at different magnifications (i.e. 18x, 160x, 500x and 1000x) and at a distance of 4 mm from the instrument's tip before being analyzed by four observers. Presence of disruption of cutting edge, crack, craters and unwinding was assessed and submitted to Fisher's exact test. Both systems showed manufacturing defects and cracks. The presence of disruption of cutting edges was major in WaveOne files from the sixth use, whereas One Shape NG files showed more unwinding. Only preparation time using WaveOne files was influenced by the number of uses. One can conclude that WaveOne files had more disruption of cutting edges and took longer time for root canal preparation from the sixth use onwards, whereas the One Shape NG files showed more unwinding at the tenth use.