Enterococcus faecalis and Candida albicans have been associated with cases of secondary and persistent root canal infections, been resistant to calcium hydroxide. So, the evaluation of the susceptibility of these microorganisms biofilms to new drugs is an important practice for establishing the best drug and consequently success of treatment. For this, in vitro biofilm formation of E. faecalis and C. albicans was induced separately on blocks obtained from bovine teeth. After the period of specimen incubation for biofilm maturation, the samples were immersed in the pastes: 1 – calcium hydroxide (CH), 2 – chlorhexidine (C), 3 – ciprofloxacin (CP), 4 – metronidazole (MT), 5 – ketoconazole (KE), 6 – double antibiotic (DB), 7 – triple antibiotic (TA), 8 – ciprofloxacin + ketoconazole (CPKE); 9 – ciprofloxacin + metronidazole + ketoconazole (CPMTKE), 10 – metronidazole + ketoconazole (MTKE), and 11 – control (CO) for 7 days. Next, the specimens were live/dead stained for analysis by confocal microscopy. By means of the Bioimage program, the biovolume and percentage of live cells were measured. The data were statistically compared (p = .05). For the C. albicans biofilm, the best antimicrobial action was found for MTKE, CPKE, and MT groups. Whereas for E. faecalis biofilm, the lowest percentage of live bacteria was found in TA, DB, and CP groups; however, KE, CPKE, CPMTKE, and MTKE groups shown to be effective. The authors concluded calcium hydroxide paste and chlorhexidine was not effective for both biofilms. The MTKE and CPKE pastes presented effectiveness for both biofilms. TA and DB pastes were effective just in the E. faecalis biofilms.