Cryptosporidium spp. and Cyclospora cayetanensis have emerged as important causes of epidemic and endemic diarrhea in immunocompetent and immunocompromised hosts. The exact modes of transmission in certain rural areas are still unclear. Reports of water-borne and food-borne outbreaks suggest that fecally contaminated water or food acts as a vehicle of transmission. Two hundred stool samples of patients with gastroenteritis from four health centers in a rural area of Jordan were examined using formalin-ethyl acetate concentration, wet preparation, and modified acid-fast staining methods. Oocysts of C. cayetanensis and Cryptosporidium spp. were found in 6% and 8% of the samples respectively, mainly those of children. Parasites such as Entamoeba histolytica, Giardia lamblia, and other enteropathogens were also observed. The results reflect the seasonality of natural cyclosporiasis and cryptosporidiosis, being higher in the spring. The risk factors that were found by the Fisher test to be significant and might be associated with illness are the source of drinking water, contact with animals, and eating unwashed vegetables ( p<0.028, p<0.0005, p<0.00005 respectively).