Anemia is estimated to affect one-half of school-age children in developing countries. The school years are an opportune time to intervene, and interventions must be based on sound epidemiologic understanding of the problem in this age group. We report on the distribution of iron deficiency and anemia across age, sex, anthropometric indexes, and parasitic infections in a representative sample of 3595 schoolchildren from Pemba Island, Zanzibar. Iron status was assessed by hemoglobin, erythrocyte protoporphyrin (EP), and serum ferritin concentrations from a venous blood sample. Overall, 62.3% of children were anemic (hemoglobin < 110 g/L), and 82.7% of anemia was associated with iron deficiency. The overall prevalence of iron-deficient erythropoiesis (EP > 90 mumol/mol heme) was 48.5%, and the prevalence of exhausted iron stores (serum ferritin < 12 micrograms/L) was 41.3%. In bivariate analyses, iron status was slightly better in girls than in boys, and was better in children aged 7-11 y than in those older or younger. Hemoglobin but not EP or serum ferritin concentrations were lower in stunted children. Infection with malaria, Trichuris trichiura, Ascaris lumbricoides, and hookworms were all associated with worse iron status; the association with hookworms was strongest by far. In multivariate analyses, hookworm infection intensity was the strongest explanatory variable for hemoglobin, EP, and serum ferritin. Sex, malarial parasitemia, A. lumbricoides infection, and stunting were also retained in the multivariate model for hemoglobin. Twenty-five percent of all anemia, 35% of iron deficiency anemia, and 73% of severe anemia were attributable to hookworm infection; < 10% of anemia was attributable to A. lumbricoides, malaria infection, or stunting. We conclude that anthelminthic therapy is an essential component of anemia control in schoolchildren in whom hookworms are endemic, and should be complemented with school-based iron supplementation.