In India, medicinal plants form the basis of many indigenous traditional systems of medicine. The natural alternatives for root canal irrigants are biodegradable and safe with fewer side effects. Sodium hypochlorite (NaOCl) has long been the irrigant of choice for endodontic procedures as it dissolves necrotic and vital tissue.It has an unpleasant odour and taste and it is highly toxic to periapical tissues. Azadirachta indica (neem) is one of the most versatile medicinal plants with wider antibacterial spectrum. Morinda citrifolia (MCJ) commonly called as Noni has a broad range of antimicrobial, antitumour and immune enhancing effects. When compared to NaOCl, Noni is less toxic and equally effective in removing the smear layer. Aim: To compare the antimicrobial efficacy of sodium hypochlorite (2%), neem leaf extract (3%) and Morinda citrifolia (6%) against E. faecalis and C. albicans using the agar diffusion method. Material and methods: Group 1- Sodium hypochlorite (2%) Group 2- Alcoholic neem leaves extract (3%) Group 3- Morinda citrifolia (6%) The stock cultures of E. faecalis and C. albicans were used for the study. The cultures were grown overnight at 37C in BHI broth for E.fecalis and peptone agar for C. albicans. They were spread onto the agar plates. Agar well diffusion method was done. Each of the test specimens was added to the respective wells and incubated. Zone of inhibition was measured for each solution after 24 hours. The cultures were repeated for three times and the average values were found. Results: Inhibition zones for E. fecalis- Neem (18mm) > NaOCl (14mm) > Morinda (12.5mm) Inhibition zones for C. albicans- Neem (9mm) >NaOCl (7.5mm) > Morinda (6mm) Conclusion: In vitro observation of neem's effectiveness appears promising and being a herbal product, it is expected to be safe to use neem leaf extract clinically as an endodontic irrigant. Keywords: Anti-microbial efficacy, Azadirachta indica, Morinda citrifloia