
Introduction: The development of new endodontic technology is aimed at increasing ease and practicality. However, the basic principles of disinfection should also be considered because the presence of residual necrotic tissues and bacteria in the root canal has a direct effect on the outcome of endodontic therapy. Aim of the study: To evaluate the effect of two rotary systems versus manual instrumentation on the reduction of Enterococcus faecalis count in the root canal. Materials and Methods: Forty extracted mandibular premolars with single canals were inoculated with Enterococcus faecalis suspension (ATCC 29212). Specimens were divided according to the instrumentation technique into four parallel groups (n=10). Group I: ProTaper Next, Group II: One Shape Apical, Group III: K-Flexofiles and Group IV: No instrumentation (control group). Irrigation was performed using sterile saline solution. Bacterial samples were taken before, immediately after and one week after instrumentation. The samples were cultured on blood agar plates, incubated and the colony forming units were counted. Data was collected and then statistically analyzed. Results: Significant bacterial reduction was observed in Groups I, II and III compared to the control group. Groups I, II and III also showed significant reduction in the bacterial count in immediate and final samples compared to the initial samples. No significant difference was found between the three groups immediately after instrumentation. However, Group I showed significantly higher bacterial reduction one week after instrumentation, compared to the initial sample and the other three groups. Conclusions: All instrumentation techniques were equally significantly effective in reducing intracanal E. faecalis count immediately after instrumentation. After one week, bacterial growth was observed in all the groups; however, ProTaper Next significantly demonstrated the least amount of bacterial growth compared to One Shape Apical and K-Flexofiles.