Methods and Material: The sample size consisted of 45 distobuccal roots of maxillary molars. The canals were sterilized and bio mechanically prepared to ISO #20 and later infected with an inoculation of a culture of E. faecalis. After the incubation period samples were collected from these canals and counted for CFUs. According to the type of file systems used, the samples were divided into three groups (n=15). Three roots were left uncontaminated and uninstrumented which served as the control to demonstrate the sterility of the canal after sterilization. After instrumentation, the bacterial samples were again collected from the roots and evaluated for CFU count.

Statistical analysis: The data obtained from the three groups was statistically evaluated by using one way ANOVA test.

Results: All of three groups demonstrated an efficient mean reduction in CFU. Mtwo system produced a 76.68% decrease in CFUs, Pro Taper system 70.56% and the Neoendo Flex system produced a decrease of 68.83% in E. faecalis count. Mtwo showed higher percentage reduction than Pro Taper and Neoendo Flex. The difference between Mtwo, Pro Taper and Neoendo Flex was statistically significant (P<0.001).

Conclusion: All the three systems included in the study showed a significant reduction in the number of bacteria in mechanical disinfection of root canals after instrumentation.