Aims & Objectives:The purpose of this study was to investigate the effects of 5.25% sodium hypochlorite (NaOCl) and 2% chlorhexidine (CHX) on Gutta-percha and Resilon cones using an atomic force microscope (AFM).Materials and Methods:Gutta-percha cones (n = 15) and Resilon cones (n = 15) were cut 3 mm from their tip, attached to a glass slide with cyanoacrylate glue and immersed in 5.25% NaOCl and CHX for 1, 5, 10, 20 and 30 min. Five each of Gutta-percha and Resilon cones not treated with any disinfectant were used as control. The analysis of the surface topography was performed on the region between 1 and 2 mm from the tip using the AFM. The root mean square (RMS) parameters for contact mode imaging were measured. The differences between RMS values were tested by SPSS-16.0 version statistical software [IBM SPSS (Statistical Product and Service Solutions) Data Software, Chicago, US] using Kruskal-Wallis ANOVA, Mann-Whitney U-test and Wilcoxon matched pairs test.Results:There was no deterioration in the surfac e topography of Gutta-percha and Resilon when treated with 2% CHX in comparison to baseline (P < 0.05). Resilon exhibited no deterioration in topography when immersed in 5.25% NaOCl. There was a significant decrease in the mean RMS values of Gutta-percha treated with NaOCl from the control at time intervals of 1, 5, 10, 20 and 30 min.