Mesial roots and isthmuses of mandibular molars are difficult areas to obtain adequate disinfection of root canal walls, and consequently microorganisms can survive treatment. The present study compared, through real-time polymerase chain reaction (qPCR), the effectiveness of TRUShape (TS) (Dentsply Tulsa Dental Specialties, Tulsa, OK) and Vortex Blue (VB) (Dentsply Tulsa Dental Specialties, Tulsa, OK) in removing Enterococcus faecalis (E. faecalis) from the mesial canals and isthmuses of mandibular molars. Fifty extracted human lower molars were inoculated with E. faecalis OG1RF for 14 days, and then an initial bacterial sample was collected with paper points from mesiobuccal and mesiolingual canals and isthmuses. The specimens were randomly divided into four groups (n = 10 teeth; 20 canals each), according to instrumentation system: TS 25/0.06, TS 30/0.06, VB 25/0.06 and VB 30/0.06. The remaining 10 teeth were divided between positive control, inoculated teeth without instrumentation or irrigation, and negative controls, teeth without inoculation. After instrumentation, the final sample was taken using paper points and DNA was isolated. Primers specific for E. faecalis were used for qPCR. The bacterial reduction between pre- and post-instrumentation was calculated. One-way analysis of variance (ANOVA) with Bonferroni’s multiple-comparisons tests were for statistical analysis with significance of (p 0.05). All file systems were able to reduce the load of E. faecalis from the prepared root canals, however, TS size 30 removed significantly more bacteria than size 25. Interestingly, regardless of the size, TS files removed significantly more E. faecalis biofilm (p 0.05) than did VB files (63.7% vs 50.8% for size 25, and 69.5% vs 56% for size 30). In conclusion, when combined with irrigation, TS file system is more effective than VB in reducing E. faecalis biofilms from mesiobuccal and mesiolingual canals and the isthmuses of mandibular molars.