BACKGROUND: Anemia is a major public health problem in preschool children in Alagoas, Brazil, especially in the younger population, because of a positive correlation between hemoglobin level and age. However, due to the lack of studies, it is not known how widespread this condition is among older children or how it is associated with socioeconomic status. The aim of this study was to investigate the prevalence of and factors associated with anemia in school children from the city of Maceió, Alagoas state, Brazil. The analysis was stratified to identify any effect modification according to whether they attend public or private schools. METHODS: A cross-sectional study was conducted using probability sampling of 1518 children (9.8 ± 0.5 years of age) attending public (n = 931) and private (n = 587) elementary schools in the municipality. Semi-structured questionnaires were used to obtain socioeconomic, demographic, anthropomorphic, hemoglobin (Hb), and dietary data. Anemia (Hb <11.5 g/dL) was the dependent variable. The measure of association used was prevalence ratio (PR) and respective CI95 %, calculated by Poisson regression with robust variance adjustment, for the crude and adjusted analyses. RESULTS: The prevalence of anemia was found to be higher amongst the public school children than the private school children (10.8 % vs. 7.0 %; PR = 1.54; CI95 %: 1.1; 2.2). At the public schools, the variables that remained significantly associated with anemia after the multivariate analysis were "consumption of fruits/fruit juices < 2 portions/day" (PR = 2.19; CI95 %: 1.18; 4.06) and "male" (PR = 1.51; CI95 %: 1.001; 2.30). At the private schools, these variables were "working mother" (PR = 2.83; CI95 %: 1.23; 6.52) and "monthly school fees < R$ 188.00" (PR = 3.20; CI95 %: 1.46; 7.03). CONCLUSIONS: In the population under study, anemia constitutes a major health problem, especially among children from public schools. Considering the associated factors and the fact that these children are in a school environment, the promotion of healthy eating habits could constitute an important approach for reducing the prevalence of anemia.