The aim of this study was to provide baseline information of the epidemiological situation of malaria in Madagascar using serological markers. We carried out cross-sectional studies in schoolchildren from eight sites in the four different malarious epidemiological strata of Madagascar. We studied the prevalence of anti-MSP1 antibodies to assess the burden, and anti-CSP antibodies to estimate the transmission intensity, of malaria. The overall prevalence of each antibody tested was 46.1% for anti-PfMSP-1, 15.2% for anti-PvMSP-1, 14.9% for anti-PfCSP, 4.9% for anti-PvCSP and 2.4% for anti-PmCSP. The prevalence of the five antibodies varied significantly between the sites (P<10(-6)). We also found significant effects of ethnic origin on the prevalence of anti-PfMSP1 antibodies. With regular testing in the same target populations, this data will be particularly useful for managing the elimination strategy supported by the Malagasy Government.