Most root canal procedures are anatomically complex, resulting in insufficient removal of the necrotic pulp by mechanical root canal shaping. This study evaluated the use of antibiotics as canal irrigants for removal of susceptible intracanal bacteria, using an Enterococcus faecalis biofilm model. Enterococcus faecalis biofilm was developed in the root canal and test tube. For the experiments, sodium hypochlorite (NaOCl), augmentin and erythromycin were used as intracanal irrigants. The test tubes and canals were prepared and irrigated with phosphate buffered saline (PBS), NaOCl, augmentin and erythromycin. Bacterial samples were collected after irrigation in the test tube models on day 1, and from the tooth model on days 1, 4 and 7. The surface of each sample and attached pattern of the bacteria was also analyzed by examining under scanning electron microscopy (SEM). The antibacterial study using 10 ml test tubes (n=10) revealed that 5% NaOCl, augmentin and erythromycin inhibited bacterial growth relative to PBS. In the tooth model, NaOCl, augmentin and erythromycin inhibited bacterial growth significantly (all p<0.05) at days 4 and 7, relative to PBS. Compared to day 1, bacterial density of all groups reduced at day 7, and changes in cell morphology were observed in all experimental groups. Our studies revealed evidence of significant differences in the antimicrobial efficacy at days 4 and 7, upon irrigation with augmentin and erythromycin versus PBS, in root canals infected with E. faecalis.