Food-borne parasitic diseases, many known to be more prevalent in poor countries with deficient sanitary conditions, are becoming common worldwide. Among the emerging protozoan parasites, the most prominent is Trypanosoma cruzi, rarely reported in the past to be transmitted by the oral route but currently responsible for frequent outbreaks of acute cases of Chagas disease contracted orally and characterized by high mortality. Several other food-borne protozoans considered emerging include the apicomplexans Toxoplasma gondii and Cryptosporidium, as well as Giardia and Entamoeba histolytica. Here, the interactions of these protozoans with the mucosal epithelia of the host are discussed.