Background: Success of endodontic treatment depends on complete debridement and disinfection of root canal space. Objective: The evaluation of the efficiency of the Chlorhexidine and ozone gas in the elimination of Candida Albicans in the root canals. Hypothesis: Is Chlorexidine treatment more effective than ozone gas treatment? Materials and methods: In this study we inoculated 20 teeth with C. albicans. All teeth were washed with 10 cc of sterile saline solution. The root canals were incubated with Brain-Heart infusion broth at 37°C for 24 hour. 20 single-rooted human teeth were prepared using Mtwo instrument. In the first group (n=10) as an irrigating agent we used 10 cc of 2% CHX solution and in the second group (n=10) as an irrigating agent we used ozone gas. Statistical analysis was performed using IBM SPSS Statistics 23.0. Data were analyzed by one-sample t-tests. The significance level (α) was set at 0.05, with a confidence interval (CI) of 95%, whereas P-value and analysis of variance (ANOVA) are used to compare independent samples. Results: Chlorhexidine treatment reduced significantly the amount of C.albicans (P=0.002) compared with the group treated with ozone gas (P=0.005). By reducing the number of treatments in time period, the difference between the effects of two irrigants is increased, dominating the chlorhexidine treatment. Conclusion: The efficiency of the treatment with chlorhexidine is maximal and the colony forming units falls significantly and we recommend using this treatment in comparison to the ozone gas treatment.