Background: To assess the antibacterial effect of ethanolic extract of propolis, miswak and green tea compared to sodium hypochlorite and chlorhexidine as root canal irrigants against E.faecalis biofilm using laboratory culturing and scanning electron microscope (SEM). Materials and Methods: fifty, human, single canalled teeth were used. The crown of each tooth was sectioned. After root canal preparation and sterilization, the roots were infected with E. faecalis. Roots inoculated with E.faecalis were incubated at 37Co for 7 days. Then root canals were instrumented using Revo S NiTi files and different irrigants: Sodium hypochlorite 3% (NaOCl), 2% chlorhexidine (CHX), 20% ethanolic extract of Egyptian propolis, 20% ethanolic extract of Miswak and 20% ethanolic extract of Green tea. Root canals were sampled before (S1) and immediately after the chemo- mechanical preparation (S2). The data obtained collected, tabulated, and statistically analyzed. Results: NaOCl group (2.56±2.74) showed the lowest mean Log10 of bacterial counts, it was non-statistically significant different from CHX group (3.83±2.37), Propolis group (4.62±1.88) and Miswak group (4.93±2.01). NaOCl group showed statistically significantly lower mean Log10 of bacterial counts than Green tea group (5.82±0.16) and Saline group (6.39±0.30). Conclusion: Propolis, Salvadora Perisca and green tea offer a promising natural antimicrobial alternative and may serve as a new endodontic irrigants.