Summary. Research shows negative trends in health of schoolchildren: increasing morphofunctional disorders, mental and behavioral disorders, acute and chronic somatic morbidity, maladaptation syndrome, as well as negative health dynamics and the highest morbidity among middle school students. The aim of the study was to determine the state of health of students during basic school stage, under the conditions of using traditional and meritocratic education systems. Materials and Methods. The study involved 266 students of general secondary education institutions aged 10-14 years. Results. Analysis of the level of pathological lesions in different educational programs established the highest level for diseases of the endocrine system with an increase in pathology in the dynamics of learning by 220.8 ‰ in traditional education and 172.8 ‰ in meritocratic education. Pathology of the eye and adnexa was more common among students throughout the meritocratic program with its significant increase in both education systems, while the number of digestive diseases increased more significantly in traditional education (p <0.01). The decrease in pathological lesions occurred only in diseases of the respiratory system with meritocratic education. There was a significant increase in the percentage of the second group of health (from 62.3 ± 5.5% to 77.9 ± 4.7%) in education on the meritocratic system, and insignificant increase in traditional education due to reduced proportion of healthy children. Under the conditions of the traditional education system, the number of cases of acute diseases was higher (p <0.05-0.01) and a significant increase in their total duration was determined at the end of the 5th and 6th grades (p <0.05). At the same time, all indicators of acute morbidity decreased during years of study 7 to 9, regardless of gender, educational program and type of general secondary education institution. Conclusions. Studying under the conditions of the meritocratic system was accompanied by a more intensive increase in the prevalence of diseases of the eye and adnexa, but a decrease in pathological lesions of the respiratory system. During the implementation of the traditional educational program, a more significant increase in the prevalence of digestive diseases was registered, as well as the number of cases and the total duration of acute diseases at the end of the 1st and 2nd year of basic school. Comparative analysis of morbidity indicators revealed a significant impact of intensification of the educational process on the progression of ophthalmic pathology, chronic diseases, against the enduring general trend as to the dynamics of acute morbidity and the overall structure of pathological lesions.