Enterococcus faecalis has been suggested to be an important etiological agent in endodontic failures. The purpose of this study was to evaluate the effectiveness of chlorhexidine- or antibiotics-based medications in eliminating E. faecalis biofilms. One-day and three-day biofilms of E. faecalis were induced on cellulose nitrate membrane filters. Each biofilm-containing membrane was thoroughly covered with 1 ml of the test medications and incubated for 1 day at 37 degrees C. Treated biofilms were then aseptically transferred to vials containing a neutralizing agent in saline solution and vortexed. Suspensions were 10-fold diluted, seeded onto Mitis salivarius agar plates, and the colony-forming units counted after 48 h of incubation. There were significant differences between the formulations tested. The association of clindamycin with metronidazole significantly reduced the number of cells in 1-day biofilms. However of all medications tested, only 2% chlorhexidine-containing medications were able to thoroughly eliminate most of both 1-day and 3-day E. faecalis biofilms.