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These Apicomplexan parasites have emerged as an important cause of chronic and fatal disease in immunodeficient individuals, in addition to being investigated as possible triggers of inflammatory bowel disease. <jats:italic>T. gondii<\/jats:italic> disseminates to the brain and other tissues after infection, whereas <jats:italic><jats:styled-content style=\"fixed-case\">C<\/jats:styled-content>.\u00a0parvum<\/jats:italic> remains localized to the intestine. In the following review, we will discuss the pathogenesis of these parasitic diseases in the small intestine, the site of initial invasion. 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