Over a 2-year period, the prevalence and clinical characteristics of Cryptosporidium-associated diarrhea in the Nile River Delta of Egypt was studied. A stool sample was obtained from children with diarrhea attending one of two study hospitals and of the 1275 children evaluated, 214 (17%) were found to be infected with Cryptosporidium. Younger age was a risk factor for developing Cryptosporidium-associated diarrhea. Children <12 months of age were 2.4 times more likely to be infected with Cryptosporidium (p<0.01) and children 12 to 23 months were 1.9 (p<0.05) times more likely to be infected with the organism as compared to older children. Breastfeeding had a trend towards protection against Cryptosporidium-associated diarrhea (p=0.07). Clinical findings associated with Cryptosporidium diarrhea included vomiting, persistent diarrhea and the need for hospitalization. Our data suggest that Cryptosporidium is common in Egyptian children and may be associated with severe diarrhea.