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The purpose of this study was to compare the ability of a mixture of a tetracycline isomer, an acid, and a detergent (MTAD) with that of sodium hypochlorite (NaOCl) to disinfect human root canals that had been contaminated with whole saliva. One hundred and thirty-two root canals of extracted human teeth were cleaned and shaped using the passive step-back technique and rotary NiTi files. The smear layer was removed, and the teeth were autoclaved. Six autoclaved samples were transferred to sterile broth without contamination with saliva to serve as negative controls. Whole saliva was used to contaminate the root canals of the rest of the samples for 48 h. Six of these contaminated samples were irrigated with Brain Heart Infusion (BHI) broth and served as positive controls. The rest of the contaminated specimens were then divided into two experimental groups of 60 teeth each. In one group, the canals were irrigated with 1 ml MTAD, and the samples were immersed in 2 ml of the same solution for 5 min. In the second group, the specimens were similarly treated with 5.25% NaOCl. All samples were washed in BHI broth and then placed in another tube containing BHI broth and incubated for 96 h. Disinfection of the samples was determined based on presence or absence of turbidity in the broth 96 h later. Twenty-three of 60 teeth treated with NaOCl remained infected. Only one of 60 teeth treated with MTAD remained infected. Statistical analysis of the data using the Chi-square test showed a significant difference between the two groups (p < 0.0001).