Because of its efficacy in inactivating waterborne protozoan cysts and oocysts, ozone is frequently used for disinfection of drinking water. The effect of ozone on cysts of Giardia lamblia was investigated in gerbils (Meriones unguiculatus), using an infectivity assay by scanning electron microscopy, immunoblotting, and flow cytometry. Cysts recovered from experimentally infected gerbils were exposed to an initial ozone concentration of 1.5 mg/L for 0, 30, 60, and 120 sec. This treatment resulted in a dose-dependent reduction in cysts concentration, loss of infectivity in gerbils, and profound structural modifications to the cyst wall. Exposure for 60 sec or longer resulted in extensive protein degradation and in the disappearance of a cyst wall and a trophozoite antigen.