Intensification of the educational process is one of the risk factors for increasing the prevalence of morphofunctional disorders, acute and chronic somatic morbidity, mental and behavioral disorders, maladaptation syndrome. Many researchers have found a negative chronological dynamics of school health and a high incidence among secondary school students. The purpose of the study is a comparative analysis of the structure and dynamics of morbidity of children during secondary school. The study involved more than 266 students of secondary schools aged 10 to 14 years. The state of health was assessed according to preventive medical examinations conducted by specialists of the Institute of Child and Adolescent Health of the National Academy of Medical Sciences of Ukraine with the informed consent of parents and according to the bioethical norms of the Helsinki Declaration (as amended in 2013). Statistical data processing was performed using the licensed package SPSS Statistic v.20 using Student’s t test. The highest level of morbidity was found in diseases of the endocrine system (468.4±39.7‰), the organ of vision and the appendix (322.8±37.2‰), the circulatory system (310.1±36.8‰) and respiration (303.8±36.6‰). Among girls, endocrine (520.7±57.7‰) and ophthalmological pathology (386.7±56.2‰) were more often registered, and among boys – mental and behavioral disorders (168.7±39.9‰; p<0.05). During the training, negative dynamics was determined for diseases of the endocrine system (due to a probable increase in their number among boys, at p<0.05), diseases of the digestive system, eye and appendages due to decreased visual acuity (p<0.01). In the structure of endocrine pathology, 60% were thyroid diseases in both sexes, and the prevalence of grade 1 obesity was higher among boys (p<0.05). Mental and behavioral disorders were mainly represented by disorders of activity and attention in adolescent boys, sleep disorders – in girls; hyperkinetic behavioral disorders – in both sex groups. Gender features in the structure and dynamics of morbidity of secondary school students to a greater extent in diseases of the endocrine system, eye and appendix with a general negative tendency to increase the prevalence of these groups of diseases.