In this study, we evaluated the effectiveness of 1 and 5.25% NaOCl solutions, with or without surfactant, in disinfecting gutta‐percha cones. Surface changes of the gutta‐percha cones after disinfection were also assessed under scanning electron microscopy (SEM). One‐hundred and eight gutta‐percha cones previously contaminated with Enterococcus faecalis were left in contact for 30 s or 1 min with the following solutions (n = 12): 1% NaOCl; 1% NaOCl + 2% cetrimide; 5.25% NaOCl; 5.25% NaOCl + 2% cetrimide. Positive control group was composed by the remaining contaminated cones (n = 12), and the negative control group by noncontaminated cones (n = 12). The cones were kept in Eppendorf tubes containing Trypticase Soy Broth at 37°C for 24 hr, and then, the presence of turbidity was analyzed. Ten additional cones (n = 2) were observed under SEM to evaluate surface changes after 1 min of disinfection. The data analysis (Kruskal–Wallis test, α = 5%) demonstrated that regardless the presence of surfactant, the NaOCl solutions used were effective in the disinfection when cones were immersed for 1 min. However, at the 30‐s period, only the 5.25% NaOCl solution was effective. SEM analysis demonstrated that NaOCl solutions promoted the formation of sodium chloride crystals on cones surface, less visible when the 1% NaOCl associated to surfactant was used. The addition of surfactant did not affect the disinfection capacity of NaOCl solutions. However, the surfactant has apparently inhibited the sodium chloride crystals deposition on the cones surface when associated to 1% NaOCl solution.