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As part of a community-based, group-randomized, controlled trial of insecticide-treated bed nets (ITNs) in an area with intense malaria transmission in western Kenya, a birth cohort (n 833) was followed monthly until the age of 24 months to determine the potential beneficial and adverse effects of reduced malaria exposure during pregnancy and infancy. Malaria transmission and morbidity were comparable pre-intervention. The ITNs reduced malaria attack rates (force of infection) in infancy by 74%, and delayed the median time-to-first parasitemia (4.5 to 10.7 months; P< 0.0001). The incidence of both clinical malaria and moderate-severe anemia (hemoglobin level< 7 g/dL) were reduced by 60%(P< 0.001 for both). Protective efficacy was greatest in infants less than three months old and similar in older infants and one-year-old children. Efficacy was lowest in the dry season. Infants from ITN villages experienced better height and weight gain. In areas of intense perennial malaria transmission, ITNs substantially reduce exposure to malaria and subsequent malaria-associated morbidity in children less than 24 months old. Reduced malaria exposure during infancy did not result, with continued ITN use, in increased malaria morbidity in one-year-old children.