Aim: The aim of this study was to evaluate the ability of XP-endo Finisher (XPF) to supplement the removal of bacteria and endotoxin from primary infected root canals after instrumentation. Methodology: This randomized and blinded controlled trial included eight subjects. Instrumentation was performed using Vortex Blue or XP-endo Shaper, followed by supplemental instrumentation with XPF. All canals were irrigated with 2.5% sodium hypochlorite. Bacterial and endotoxin samples were taken using sterile paper points. Samples were collected before and after instrumentation and after XPF. Results: Bacteria was present in all root canals. After XPF, bacterial mean was reduced from 255 ± 311.82 CFU/mL to 2.5 ± 7.07 CFU/mL (p= .056). Endotoxin was detected in all root canals by the LAL method (KQCL test). After XPF, endotoxin mean was significantly reduced from .85 ± .26 EU/mL to .03 ± .01 EU/mL (p= .00004). Conclusion: The findings of this study showed that the supplemental use of the XP-endo Finisher after root canal instrumentation was effective in significantly reducing endotoxin but not bacteria present in primary endodontic infections.