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Cryptosporidium parvum and Giardia lamblia are protozoan parasites which cause enteric infections in humans and animals. Oocysts and cysts of these parasites are frequently present in surface water and outbreaks caused by waterborne oocysts have been documented. Although the response of oocysts to chemical disinfectants has been characterized, the molecular mechanisms leading to inactivation have not been studied. Multiple analytical methods were used to study at the structural and molecular level the inactivation of oocysts and cysts exposed to ozone and chlorine. Purified oocysts and cysts were exposed to these disinfectants under controlled temperature and pH conditions. Following exposure, parasite viability was tested in neonatal mice or cell culture, and in gerbils, respectively. The integrity of the oocyst wall, of the nucleic acid (DNA and RNA), and selected surface and internal proteins was examined using electron microscopy, PCR/RT PCR, Western blotting and flow cytometry. Includes 10 references, figures.