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The natural history of Giardia lamblia and Cryptosporidium infections were determined in a cohort of 164 Bedouin children, from a population not previously studied, which is in transition from nomadism to a settled life style. Stools were sampled monthly from birth to two years of age and at all diarrhea episodes. The risk of infection with G. lamblia and Cryptosporidium infection by age two was 91.5% and 48.8%, respectively. Cryptosporidium prevalence was 3–4% at all ages, whereas G. lamblia prevalence was > 30% after age one. Giardia lamblia and Cryptosporidium asymptomatic detection rates were high, 28.5% and 1.6%, respectively. Detection of G. lamblia was higher in diarrhea episode samples obtained before six months of age, but after that age and overall, the detection was lower than in nondiarrhea samples (odds ratio [OR] = 0.8, 95% confidence interval [CI] = 0.7–0.9, P < 0.05). Detection rates of C. parvum were higher in episode-related samples in all age groups (OR = 2.8, 95% CI = 1.9–4.2, P < 0.05) and infections in boys were more frequently symptomatic than in girls. While G. lamblia does not appear to be a consistent pathogen in this population where it is hyperendemic, Cryptosporidium has been shown to be an important cause of diarrhea in young children in the community.