Introduction. High loads, intensification of education, characterize the modern educational process and contribute to the negative dynamics of the health indices of modern schoolchildren. The aim of the study is to investigate the features of the autonomous and thyroid status of schoolchildren exposed to the different intensity of the educational process. Material and methods. The objects of the study were schoolchildren with the different intensity of the educational process, students of schools. Hygienic evaluation of the educational process was carried out taking into account the requirements of Sanitary Regulations and Norms 2.4.2.2821-10. The data analysis of the survey, laboratory studies, electrocardiography, cardiointervalography and ultrasound scanning of the thyroid gland was performed. Results. The reduction of the duration of small changes, the excess of the volume of daily and weekly academic load up to 20.0% with a comparative hygienic assessment of the educational process regimes, in schools with an in-depth study of the subjects of the physical and mathematical cycle. Characterized by a large expenditure of time on homework, shorter sleep, high involvement in the additional educational process for students of specialized schools. Arrhythmias were by 1.7 times more common in students of the physical and mathematical school. Relative risk increased by 4.6 times. The activity of the sympathetic part of the autonomic nervous system was found to be elevated in 50% of schoolchildren enrolled in an in-depth program. Violations of the volume and structure of the thyroid gland occurred up to 2.6 times more often. The relative risk of activating the synthesis of antibodies to thyroglobulin and thyroperoxidase was higher by 5.7 times. Relationships are established between the blood level of cortisol and the frequency of registration of arrhythmias, the degree of activation of antibody production, the parameters of the thyroid gland. Discussion. The obtained data are consistent with the results of domestic studies and can serve as the basis for expanding the list of studies during preventive medical examinations of minors. Conclusion. In educational institutions with in-depth study of the subjects of the physical and mathematical cycle, the educational process is more intensive, which leads to the activation of the sympathetic part of the autonomic nervous system, an increase in the risk of developing autonomic dysfunctions, arrhythmias, and thyroid status disorders.