Background: The presence of pathogenic bacteria, toxins and byproducts in the root canal system show a decisive part in success of endodontic therapy. Thus, the complete removal of this bacterium is highly desirable. Several intracanal medicaments were tried to disinfect the root canal before obturation. Aim: The present study was conducted to compare Pomegranate, sodium hypochlorite, Chlorhexidine, Myrrh (Commiphora molmol), tulsi extract against Enterococcus faecalis, Fusobacterium nucleatum and Staphylococci epidermidis. Settings and Design: Cross-sectional observational prospective study. Materials and Methodology: Aqueous extract of 20% pomegranate peel, 20% pomegranate peel, 0.2% CHX, 2.5% sodium hypochlorite, Tulsi extract and Myrrh (Commiphora molmol) was used as agent against E. faecalis, F. nucleatum and Staphylococci Epidermidis. Zone of inhibition and minimum inhibitory concentration (MIC) was calculated and compared using analysis of variance and Mann–Whitney test. The information was statistically evaluated with SPSS software version 20 with P < 0.05. Results and conclusion: The mean zone of inhibition against E. faecalis, F. nucleatum and S. Epidermidis was highest in chlorhexidine and sodium hypochlorite groups compared to herbal groups. MIC was least with group III followed by group II against all bacterial species (P < 0.05). Sodium hypochlorite found comparatively better followed by chlorhexidine and other agents against E. faecalis, F nucleatum and S. epidermidis.