Abstract This study analyzed the influence of different retreatment protocols on amount of remaining filling material and amount of new sealer after endodontic retreatment. Forty mandibular molars with curved mesial roots were prepared with ProTaper Universal system, and filled with AH Plus sealer mixed with 0.1% rhodamine B and gutta-percha. After 7 days, the specimens were randomized according to the retreatment protocol (n = 10): ProTaper Retreatment System (PTR); PTR+Orange Oil (PTR+OO); PTR+Passive Ultrasonic Irrigation (PTR+PUI). No retreatment was performed in the control group (CG). After retreatment, the root canals were filled with AH Plus mixed with 0.1% fluorescein and gutta-percha. Samples were evaluated under confocal laser scanning microscopy and analyzed using Image J software. Data were analyzed using Kruskal-Wallis and Dunn tests (p < 0.05). Regarding presence of residual filling, the Kruskal-Wallis test indicated no differences among the different retreatment techniques in the perimeter and the isthmus analyses (p > 0.05); however, PTR+PUI was associated with a lesser amount of residual filling material in the canal area analysis (p < 0.05). In evaluating the new filling, the perimeter analysis showed a lesser amount of new endodontic sealer in the PTR group (p < 0.05). Moreover, the PTR+PUI group presented a significantly greater amount of new endodontic sealer in the canal area analysis (p < 0.05). There was no difference among groups in the isthmus analysis (p > 0.05). It can be concluded that PTR associated to PUI yielded better results in removing root canal filling material from the canal area. However, none of the protocols resulted in root walls completely free of remnants.