Intestinal parasites continue to be a significant health problem in both developed and developing countries. In developed countries, protozoans are more commonly the cause of gastrointestinal infections than are helminths. Some protozoan parasites have stages in which, in addition to being resistant to chemicals used for water treatment, they are small enough to pass through commonly used filtration processes. The relatively large size of helminth eggs increases the likelihood of their removal during water filtration. The direct impact of protozoan parasites on both human and animal health is considerable, and there is some evidence that infection may contribute to the development of various forms of intestinal dysregulation as well as disseminated infection, especially in AIDS patients. Protozoans of special interest, due to either their frequency of isolation or their role as emerging pathogens, includeGiardia duodenalis,Cryptosporidium parvum,Cyclospora cayetanensis, and the microsporidians,Enterocytozoon bieneusiandEncephalitozoon intestinalis.