ABSTRACT The objective of this study was to assess the change in the prevalence of anemia among under-five children attending public health services in Peru between 2012 and 2016, according to their place of residence, and to identify spatial clusters of districts with a high prevalence of anemia. An analytical cross-sectional study was carried out, based on data from the Nutritional State Information System from 2012 and 2016. We calculated the spatial autocorrelation of anemia prevalence at the district level using a global and local Moran's I index. The prevalence of anemia was 34.4% (2012) and 40.3% (2016). In 2012 and 2016, 41.7% and 46.5% of districts, respectively, had a prevalence of anemia considered a severe public health problem acording WHO criteria. Positive spatial autocorrelation was found between the prevalence of anemia and the districts for both years (2012 Moran's I: 0.22; 2016: 0.31, both p <0.001). Of the total number of districts, 8.3% (2012) and 12.6% (2016) presented a high prevalence of anemia and were also surrounded by districts with high prevalence. Anemia is a public health problem among children under five in Peru attending public health services and we identified areas with a higher concentration of anemia prevalence. Spatial patterns of anemia should be considered in the development and implementation of health interventions.