Studies on ozone disinfection have focused predominantly on bacterial and viral inactivation: very little work has been done on protozoan cysts. The available literature is inadequate to establish the kinetics of cyst inactivation with ozone. Thus, the study was designed to determine the effect of ozone concentrations, at various pH and temperature regimes, on the rate and extent of inactivation of protozoan cysts. The organisms used were the nonpathogenic soil and water amoebo-flagellate, Naegleria gruberi strain NEG, and the pathogenic and flagellated intestinal parasite of mice, Giardia muris. It was found that within the reported ranges of temperatures, pH, and ozone concentrations, the cyst inactivation kinetics deviated from Chick's law because there was an initial lag period. The rate of inactivation increased during this lag period and then declined where the inactivation rate was directly proportional to the number of viable cysts. Cysts of N. gruberi were more resistant to aqueous ozone than those of G. muris.