Objectives Adaptation processes in body of schoolchildren, along with study load and social factors, are determined by influence of climatic and geographical factors of residence region. This research has been undertaken to study the morphofunctional characteristics of schoolchildren at the age of 7–17 years. Methods The research involved 880 schoolchildren of both sexes in age from 7 to 17 years, studying in secondary school №22 in Pavlodar (Kazakhstan) and secondary school №7 in Kyzylorda (Kazakhstan). The Quetelet index of northern schoolchildren was within the norm but higher compared to southern peers. Results The Quetelet index was within the normal range for all schoolchildren, but higher among northerners. The indicator of the life index in the boys of the south was higher up to 10 years, then the adaptive possibilities of breathing decreased; in the girls in the north this indicator was higher in all periods, except for 8–9 years. The physical performance index (PWC170/kg) was higher in children from the southern region. Conclusions This study revealed significant geographical differences in the morphofunctional development of children. The obtained data served allowed establishing the “Electronic map of schoolchildren’s health” and indicated the need for systematic accounting of schoolchildren’s health indicators for effective development of differentiated prevention programs.