Objective: This study evaluated, in vitro, the degree of disinfection of the Er:YAG laser in root canals contaminated with Bacillus subtilis, Staphylococcus aureus, Enterococcus faecalis, Pseudomonas aeruginosa, and Candida albicans, for 28 days. Methods: Forty-six single-rooted human teeth were divided into five groups of eight teeth each; three teeth were used as negative controls and three as positive controls. After contamination, the root canals were prepared mechanically. Three groups were irradiated with Er:YAG laser at 100 mJ, varying the frequency (7, 10, and 16 Hz). Two groups were irrigated with 1.0% and 2.5% NaOCl solution. After treatment, two sterilized paper cones were placed in the root canals for 5 min. One cone was transferred to 2.0 mL of Letheen broth culture medium, incubated at 37 degrees C for 48 h, and then 0.1 mL of that solution was placed in 2.0 mL of brain heart infusion for 48 h to determine microbial growth. The other cone was transferred to a test pipette with peptone and water for serial dilution and spread in Mueller Hinton medium. After 24 h of incubation, the colony-forming units (CFUs) were counted. Results: There was a microbial reduction of 85.33% for the group irradiated with Er:YAG laser at 100 mJ/7 Hz, 74.58% at 100 mJ/10 Hz, and 89.50% at 100 mJ/16 Hz. For the groups irrigated with 1.0% and 2.5% NaOCl solution, 83.15% and 84.46% values of microbial reduction were obtained respectively. Conclusion: All the groups showed statistically similar results (P > 0.05%). No method totally eliminated microorganisms.