Aim: To evaluate the number of bacteria extruded apically from extracted teeth ex vivo after canal instrumentation using the two engine-driven techniques utilizing nickel-titanium instruments (ProTaper and System GT). Methodology: Forty extracted single-rooted human mandibular premolar teeth were used. Access cavities were prepared and root canals were then contaminated with a suspension of Enterococcus faecalis and dried. The contaminated roots were divided into two experimental groups of 15 teeth each and one control group of 10 teeth. Group 1, ProTaper group: the root canals were instrumented using ProTaper instruments. Group 2, System GT group: the root canals were instrumented using System GT instruments. Group 3, control group: no instrumentation was attempted. Bacteria extruded from the apical foramen during instrumentation were collected into vials. The microbiological samples from the vials were incubated in culture media for 24 h. Colonies of bacteria were counted and the results were given as number of colony-forming units. The data obtained were analysed using the Kruskal-Wallis one-way analysis of variance and Mann-Whitney U-tests, with α = 0.05 as the level for statistical significance. Results: There was no significant difference as to the number of extruded bacteria between the ProTaper and System GT engine-driven systems (P > 0.05). Conclusions: Both engine-driven nickel-titanium systems extruded bacteria through the apical foramen. © 2005 International Endodontic Journal.