Aim: The aim of this study is to analyse the effectiveness of Peroxygen Powdered System for rapid disinfection of gutta-percha cones and compare it with conventional disinfection methods. Materials and Methods: 110 gutta-percha cones of size 45 were used in the study and divided in to five groups. All the samples of gutta-percha were contaminated by immersing the cones in test tubes containing a bacterial suspension of E. faecalis strain ATCC 29212 and were incubated at 37°C for 24 hours. The initial colony forming units were determined by randomly immersing two gutta-percha cones from each group in vials containing sterile physiologic saline for 1 minute, and samples were obtained for colony forming units (CFU) count. Then, the cones from each group were tested for disinfection efficacy of the chemical agents, which were 3% sodium hypochlorite (Group I), 2% chlorhexidine (Group II), Peroxygen Powdered System [0.4 % peracetic acid] (Group III), and distilled water (Group IV) as a control, for 5 minutes. After disinfection, two cones from each group were passively rinsed in sterile water and agitated in vials containing sterile physiologic saline solution for 1 minute, and the samples were seeded in BHI agar, and incubated for 24 hours. The final bacterial colonies were counted with a colony counter. The remaining cones were stored in test tubes containing BHI broth and incubated, and then observed for turbidity for 72 hours. Conclusion: Peroxygen Powdered System containing 0.4% peracetic acid was found to be as effective as 3% sodium hypochlorite for the rapid disinfection of gutta-percha cones. Keywords: Gutta-percha, disinfection, peracetic acid