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Background: During endodontic intervention, major efforts are made to eliminate bacteria from the infected root canal system. Along these lines, keeping up the chain of asepsis is critical to anticipate sterile root canal system. Currently, gutta-percha (GP) is the most commonly used root canal core filling material. Objective: The purpose of this study was to compare the efficacy of 1% Alexidine, 2% Chlorhexidine, 5.25% Sodium Hypochlorite and saline against E.faecalis in disinfecting gutta-percha cones and to analyze the surface topography of gutta-percha cones after the rapid chemical disinfection procedure. Materials and methods: Gutta-percha cones were contaminated with E.faecalis and immersed in 1% ALX, 2% CHX, 5.25% NaOCl and 0.9% saline for 30 and 60 sec. The disinfected cones were immersed in test tubes and incubated at 37°C for 72 hours. Bacterial growth was evaluated by the presence of turbidity in the broth. Results were confirmed by sub culturing the bacterial colony. For topographical examination, the gutta-percha cones were analyzed under Scanning electron microscopy (SEM). Data was statistically analyzed using one way ANOVA. Results: ALX and NaOCl did not show growth of the tested microorganism for any observed period. CHX completely eliminated E. faecalis after 60 sec. Saline showed no antimicrobial activity. The results of SEM showed some deposits after disinfection procedure by NaOCl and CHX test solutions used. Conclusion: ALX and NaOCl were found to be the most efficient disinfecting agent in eliminating E.faecalis at different time intervals tested. The topographical examination revealed that ALX and CHX left little residue than as compared to NaOCl after 1 minute. [ABSTRACT FROM AUTHOR]