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The presence of free-living amoebae (FLA) in swimming pools has become an issue of increasing concern in recent years on account of their pathogenicity and their capacity to host other microorganisms. Effective disinfection doses for neutralizing bacteria in swimming pools are specified in the guideline (15.11.2011) put out by the Turkish Ministry of Health; however, this guideline does include any information about FLA. This study aims, therefore, to investigate the effect of different concentrations (1, 3, 5 mg/L) and contact times (0, 30, 240 minutes) of NaClO against trophozoites of FLA isolated from swimming pool waters in Turkey. Experiments were conducted using the most probable number (MPN) method. Maximum log reductions were determined to be 1.764, 2.165, and 3.388 for 1, 3, and 5 mg/L of NaClO, respectively, at 240 minutes of contact time. A. castellanii (ATCC 50373) cysts showed little log reduction (0.017) against 5 mg/L of NaClO, which has a cytotoxic effect against 3T3 cells. Thus, we recommend that new disinfection strategies be developed to try to control the presence of FLA in swimming pools. [ABSTRACT FROM AUTHOR]