From May to August 1999, we evaluated 401 patients from a pediatric hospital of Havana City. One group was composed of 113 patients with diarrhea admitted to the Gastroenterology ward and a second consisted of 288 patients without diarrhea, admitted for other reasons, and hospitalized within the same time period. Three stool samples were collected from each child and were examined using three parasitological techniques. When we compared the frequency of parasite species between both groups, we found Cryptosporidium spp. and Cyclospora cayetanensis, only in the group of children with diarrhea (P < 0.01). However, no significant differences were found in the occurrence of the other intestinal parasites (P > 0.05). In addition, in those children infected with Cryptosporidium, the diarrhea had a more prolonged duration (P < 0.01), while those infected with Cyclospora, the abdominal cramps or pain, and acute diarrhea were more frequently detected (P < 0.01). Our results showed that emerging intestinal coccidia are pathogens strongly associated in this group of children with diarrhea.