Aim: To assess clinically, radiographically and laboratory the antimicrobial effect of propolis, miswak, green tea, sodium hypochlorite and chlorhexidine on necrotic teeth with apical peridontitis. Materials and Methods: A total of 50 patients with chronic apical periodontitis in a permanent mature single–rooted tooth with a necrotic pulp were included. 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 chemomechanical preparation (S2). The samples (S1&S2) were transferred for culturing and incubation (both aerobically and anaerobically). The patients were re-evaluated both clinically and radiographically after 1, 3 and 6 months). Results: CHX group showed the highest mean % reduction in Log10 of anaerobic bacterial counts (95.5±8.0). CHX group showed non-statistically significant difference from NaOCl (86.2±16.7) and Propolis (84.4±9.7). Miswak group showed statistically significantly lower mean % reduction (75.6±19.1) than CHX group and NaOCl group, but non-statistically significant difference from Propolis group. Green tea group showed the lowest statistically significant mean % reduction in Log10 of anaerobic bacterial counts (50.10±10.35). Conclusion: Propolis, Salvadora Perisca and green tea alcoholic extracts at 20% concentration showed considerable antimicrobial effect against chronic apical periodontitis microbes generally and E. faecalis definitely.