Biocidal activities of monochloramine and peracetic acid were studied on cysts of Naegleria lovaniensis. Until recently the most commonly used biocide to disinfect cooling water systems was hypochlorite. Owing to its negative impact on the aquatic environment, ecologically less harmful alternatives have been sought. As the biocidal activity of monochloramine and peracetic acid makes them good candidates for inactivation of pathogenic Naegleria species, these biocides were tested against Naegleria lovaniensis, a relative of the pathogen Naegleria fowleri, as an alternative treatment to hypochlorite. Under laboratory conditions the biocidal activity of hypochlorite was 8- 10× stronger than that of the two investigated substances. Hypochlorite, at a concentration of 0.5 mg/L, killed 100% Naegleria lovaniensis after 1 h exposure (25°C, pH 7.3- 7.4). To achieve similar results with monochloramine and peracetic acid, 3.94 mg/L or 5.33 mg/L had to be used respectively (25°C, pH 8). It was known that the in situ biota of the biofilm, along with any organic material in the water column, had a negative impact on the efficiency of the biocides. There are, however, indications that the relative efficacy of monochloramine and peracetic acid was quite good under such conditions when compared with hypochlorite.