A comparison of the abilities of rotary versus reciprocating files to eliminate viable Enterococcus faecalis populations from the long oval root canals of extracted human teeth. Fifty teeth were contaminated and randomly distributed into two groups (n = 25 each): BT-RaCe group and WaveOne group. Two microbial samples were obtained from each tooth before (S1) and after (S2) instrumentation. The CFUs from the S1 and S2 measurements were calculated and compared between the groups. Both groups showed significantly fewer CFUs in the S2 samples (P < 0.001). In the S2 intragroup comparison, BT-RaCe resulted in significantly fewer CFUs than WaveOne (P = 0.010). In the direct comparison between the rotary multiple file shaping system and the reciprocating single-file system, the multiple file system was more efficient at reducing the microbiological load of viable E. faecalis from long oval root canals.