It has been proven that against the background of overweight and obesity, the risk of systemic chronic diseases increases. The article presents the results of studying the characteristics of the indicators of the prevalence of health disorders in schoolchildren with normal and overweight and obesity in a comparative aspect. A survey was conducted of 2159 schoolchildren aged 7–17 years, including 1096 boys/boys and 1063 girls/girls from 6 schools in the Novosibirsk region. Data on chronic morbidity and pathological afflictions of children were copied according to the data of form N 026/y-2000, for respondents in grades 10–11 with overweight (n = 100 people), data on the length and weight of the body were copied in a longitudinal aspect with the purpose of identifying the age of formation of overweight and obesity in order to build a prospective forecast of the prevalence of overweight and obesity in schoolchildren in grades 1–4 upon reaching the age of 16. Parametric statistical methods were used with the calculation of the mean (M) and standard error of the mean (±Se), as well as the methods of correlation and regression analyses. Differences were considered statistically significant at p < 0.05. The revealed differences in the prevalence of chronic diseases in children with overweight and obesity and in children with normal body weight indicate the significant importance of overweight and obesity in the formation of diseases of the circulatory system, endocrine system, food allergies and flat feet. There were no statistically significant differences in the prevalence of chronic diseases of the digestive system, nervous system, visual impairment (p ≥ 0.05). The data obtained with the predicted prospect of an increase in overweight in primary school students indicate the need for continuous development and implementation of both collective and individual prevention measures aimed at minimizing the risks of developing concomitant diseases.