Objective: This study aims to evaluate effective difference between convex triangular and rectangular cross section rotary instruments on root canal with Enterococcus faecalis (E. faecalis) colonies. Material and Methods: Samples of mandibular premolar teeth with one narrow and straight root canal were divided into 3 groups: instrumented with convex triangular cross section rotary instruments, rectangular cross section rotary instruments, and convex triangular cross section manual instruments. Each group consisted of nine samples. Standardized teeth length, instrumented to #15 K-file and sterilized. E. faecalis suspension in BHIB was standardized and then 27 root canals were contaminated. Root canals were incubated for 21 days. Every 48 hours root canals were added with BHIB. Initial samples were collected, plated in agar culture medium and incubated for bacterial count and then bacterial count was performed again. Data were collected and analyzed using Paired T-test and ANOVA test. Results: This indicates that there is a significant difference of the average number in colonies of E. faecalis before and after the instrumentation on the utilization of the rotary instrument in cross section of rectangular, convex triangular, and cross section manual of convex triangular. Conclusion: Showed there are significant differences on E. faecalis colonies amount before and after all instruments that was used and bacterial reduction amount in root canals were greater on convex triangular cross section instruments than on rectangular cross section instruments even though there was no significant difference.