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Introduction: Obturating materials exposed to the dental operating environment has been shown to be contaminated, making rapid chair side disinfection mandatory to ensure the sterility of the root canals. Objective: The purpose of this study was to investigate the effectiveness of CFC (combination of Calcium hydroxide, Flagyl and Ciprofloxacin) for the rapid disinfection of Gutta-percha and Resilon cones. Materials and Methods: Seventy new Gutta-percha and Resilon cones were randomly selected, contaminated with Enterococcus faecalis and divided into 4 group according to the irrigant used for disinfection {Group I: 5.25% Sodium Hypochlorite (NaOCl), Group II: MTAD, Group III: 2% Chlorhexidine (CHX), Group IV: CFC (a combination of Calcium hydroxide, Flagyl and Ciprofloxacin)}. All the samples were placed in a centrifuge tube with BHI broth after being washed with sterile water. The samples were then incubated for 7 days at 37oC. Samples were randomly plated on Mac Conkey agar plate and the colony count was recorded and the observations were drawn. Results: A 5.25% NaOCl required 1 minute exposure for effective disinfection of all the samples. MTAD could eliminate E.faecalis from gutta-percha samples in 30 seconds whereas it required 1 minute of exposure for Resilon cones. Both 2% CHX and CFC could not disinfect the samples with 1 minute exposure and a minimum of 5 minute exposure was required. Conclusion: A 5.25% NaOCl and Biopure MTAD required less chair side time to disinfect all the samples effectively when compared with 2% CHX and CFC.