To estimate the burden of anemia attributable to malaria, inflammation, and deficiency of iron or vitamin A during low and high malaria seasons among Zambian children. From a cohort of children (n=820), 4-8years of age participating in a randomized controlled trial of pro-vitamin A, we estimated attributable fractions for anemia (hemoglobin of <110 or 115g/L, by age) owing to current malaria or inflammation (C-reactive protein of >5mg/L, or α-1 acid glycoprotein of >1g/L, or both), and current or prior iron deficiency (ID; defined as low ferritin [<12 or 15μg/L for age <5 or >5years] or functional ID [soluble transferrin receptor of >8.3mg/L] or both) and vitamin A deficiency (retinol of <0.7μmol/L), during low and high malaria seasons, using multivariate logistic regression. Serum ferritin, soluble transferrin receptor, and retinol were adjusted for inflammation. The burden of anemia independently associated with current malaria, inflammation, ID, and vitamin A deficiency in the low malaria season were 12% (P<.001), 6% (P=.005), 14% (P=.001), and 2% (P=.07), respectively, and 32% (P<.001), 15% (P<.001), 10% (P=.06), and 2% (P=.06), respectively, in the high malaria season. In both seasons, functional ID was independently associated with more anemia (approximately 11%) than low ferritin (approximately 4%). Anemia and ID in the low malaria season, accounted for 20% (P<.001) and 4% (P=.095) of the anemia in the subsequent high malaria season. Anemia in this population is strongly linked to malaria, inflammation, and functional ID, and to a lesser extent, low iron stores. Integrated control strategies are needed.