The purpose of this study was to compare the efficacy of reciprocating and rotary techniques for removing gutta-percha and sealer from root canals. Forty straight and oval single-rooted premolars were prepared up to size 30, filled with gutta-percha and sealer, and then randomly allocated to two experimental retreatment groups: ProTaper Retreatment System (PTRS) and WaveOne System (WS). Procedural errors, time of retreatment and apically extruded material were recorded for all the roots. The roots were radiographed after retreatment. The percentage of residual material was calculated using image analysis software. The data were analyzed by Kolmogorov-Smirnov and t tests, with a significance level set at 5%. No system completely removed the root filling material from the root canal. No significant differences were observed between the systems, in terms of residual filling material in any tested third (p > 0.05). WS was faster in removing filling material than PTRS (p < 0.05). Extrusion was observed in 4 cases in PTRS and in 5 cases in WS. No procedural errors were observed in either group. It can be concluded that although no differences were observed in the efficacy of PTRS and WS for removing root filling material, WS was faster than PTRS.