It is well-known that investigation of the features of incidence among children and adolescents in certain human environment aimed at identification of promising prevention vectors in the region is a priority in the development of healthcare system and the state’s social policy. The study was aimed to explore the regional features of the pediatric population health in the regions of the Far Eastern Federal District (FEFD). A retrospective analytical study was conducted; the values and structure of incidence in children and adolescents in 11 FEFD regions were assessed. It was found that classes X (Diseases of the respiratory system) and XIX (Injury, poisoning and certain other consequences of external causes) occupied the leading places in the structure of the long-term average annual incidence by disease classes in FEFD among children aged 0–14 and adolescents aged 15–17. The lowest incidence was reported for class III (Diseases of the blood and blood-forming organs and certain disorders involving the immune mechanism). Significant differences in the long-term average annual levels of the studied indicator between age groups in FEFD and significant differences from the all-Russian values were revealed. The findings can be used to predict the health status of the younger generation and determine the strategic direction of healthcare system in the macroregion.