Objective: Several kinds of functional water are used in the fields of food hygiene and medicine. The purpose of this study was to evaluate both the disinfection and cytotoxic effects of functional water in comparison with commonly used root canal irrigants such as sodium hypochlorite solution and hydrogen peroxide solution. Method and Materials: Three kinds of functional water were examined: alkaline electrolysis water (AEW), strong acid electrolyzed water (SAEW), and hypochlorous acid water (HAW). The disinfection effect was studied using Enterococcus faecalis and Candida albicans with or without organic substance. Each kind of functional water was applied to samples, and the colony formation was evaluated. The cytotoxic effect was evaluated by mitogenic assay (MTT) and alkaline phosphatase (ALPase) activity in pulp cells. Results: SAEW and HAW showed microbicidal effects in the presence of organic substance, with an effect almost similar to sodium hypochlorite solution. AEW did not show any microbicidal effect. SAEW, AEW, and HAW at 10- and 1,000-times dilution did not inhibit the MTT assay and ALPase activity. The cytotoxicity of SAEW and HAW against pulp cells was mild compared to that of sodium hypochlorite solution. Conclusion: Functional water like SAEW and HAW have a good microbicidal effect under existing organic substance and are also mild to pulp cells. Keywords: cytotoxic effect, electrolyzed water, functional water, hypochlorous acid water, microbicidal effect, root canal irrigation