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Objectives To describe the prevalence and spatial distribution of anaemia among children aged 6–59 months in Madagascar and to explore individual-level and community-level correlates using data from the 2021 Madagascar Demographic and Health Survey.Design A population-based cross-sectional study using secondary data from the 2021 Madagascar Demographic and Health Survey. Spatial statistical methods were used to assess geographic clustering and hotspot areas of anaemia.Setting The study was conducted across community and household levels throughout Madagascar, covering both rural and urban populations within the primary and secondary healthcare delivery contexts.Participants A weighted sample of 10 683 children aged 6–59 months was included. Sampling followed demographic health survey procedures, and only children with complete haemoglobin data were analysed.Interventions No interventions were applied.Primary and secondary outcome measures The primary outcome was anaemia, defined as haemoglobin <11 g/dL. Spatial autocorrelation and hotspot analyses identified geographical clustering patterns.Results The overall point prevalence of anaemia was 47% (95% CI 45.60 to 48.36), showing significant spatial clustering (Global Moran’s I=0.136, p<0.001), with hotspots mainly in the central and southeastern regions. Differences in anaemia prevalence were observed across population subgroups, including child age, maternal education, household wealth, place of residence and nutritional status.Conclusions Anaemia among Malagasy children remains a major public health concern and shows clear geographic variation. The findings describe important differences in prevalence across regions and population subgroups, providing useful evidence for public health planning and for generating hypotheses for future analytical research.