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In the first year of a prospective community study of childhood diarrhea conducted in a semiurban area in the capital of Guinea Bissau, Cryptosporidium sp. was found in 73 (6.0%) of 1216 episodes of diarrhea. The parasite was the second most prevalent intestinal parasite, and the only one significantly associated with diarrhea (OR = 2.79, P = 0.0006). The seasonal distribution was striking, with a peak prevalence in the beginning of the rainy season (May 17.6%) when an epidemic outbreak of diarrhea started. The prevalence was highest in children younger than 18 months, an age at which prevalences of other intestinal parasites were low. This reverse age pattern may possibly be explained by the small infective dose needed to create severe infections, by air-borne transmission and by the development of protective immunity.