Introduction. Against the background of socio-economic transformations and the digitalization of education, the health indicators of students are changing, which requires in-depth research. Aim of the study: based on the longitudinal observation of the health of schoolchildren, to identify the patterns of its formation for the scientific justification of improving the medical care of students. Material and methods. From the 1 st to the 11 a grade (2005–2015), the same students (199 boys and 227 girls) of 4 Moscow schools were examined annually with the performance of anthropometry, electrocardiography, functional tests, and questionnaire to identify complaints and anamnesis; specialist doctors carried out 25,298 examinations. In addition to the analysis of morbidity, a qualitative analysis of the course of pathological processes in students was carried out to determine positive and negative dynamics. Results. Over 11 years, the prevalence of functional disorders increased by 14.7%, chronic diseases by 52.8%, the frequency of visual disturbances, diseases of the musculoskeletal system, digestive organs, neurotic reactions increased; new forms of risk behaviour and information dependence appeared. An unfavourable period of development of pathological processes in schoolchildren is training in grades 9–11. Compared with the 1990 morbidity rates obtained by similar methods, there was an increase in the prevalence of functional disorders among adolescents by 2–3 times and chronic diseases by 20–70%. When comparing physical development with peers of the second half of the XX century, the observed schoolchildren increased the average values of body length and weight with a decrease in functional indicators. Distance learning during the first wave of COVID-19 in spring 2020 has increased the prevalence of computer vision, carpal tunnel syndromes, and neurotic reactions. Discussion. The main patterns of health formation in school ontogenesis, coinciding with the change of generations and the transition to the digitalization of education, are revealed. Conclusion. The study results allow predicting an increase in the prevalence of neuropsychiatric disorders, myopia, scoliosis, computer-visual and carpal tunnel syndromes. To preserve students’ health, to counteract COVID-19, a modern model of school health care is proposed.