Objective : the study was designed to compare the antimicrobial efficacy of 5% Sodium hypochlorite solution and 10% Neem leaves extract against infected root canal microbial isolates with special reference to Enterococcus Faecalis and Candida Albicans using Agar diffusion method. Materials and Method: A total of 50 patients requiring endodontic therapy with chronic periapical infection were selected and samples were isolated under strict aseptic protocol from the root canal systems. The samples were subjected to check the antimicrobial efficacy of Group A – 5% Sodium hypochlorite solution and Group B – 10% Neem leaves extract and Group C – distilled water as a control group. Agar well diffusion method was used for incubation and zones of inhibition was recorded. Results were subjected to ANOVA test and other statistical analysis using SPSS software. Results : It appeared that Group A and Group B are significantly effective in antimicrobial efficacy against E. Faecalis and C. albicans except Group C where no zones of inhibition was seen. The difference between scores obtained with Sodium hypochlorite solution and Neem leaves extract was statistically significant (P=0.05) Conclusion : 5% Sodium hypochlorite solution and Neem leaves extract has significant antimicrobial effect against E. faecalis and C. albicans with neem being possessing a significant property of biocompatibility to oral and periapical tissues