In the context of declining birth rates, maintaining the health of children with disabilities and special health needs (SHN) is one of the state’s tasks. A comprehensive assessment of children's health is essential for solving this problem. The study aimed to justify the inclusion of quantitative indicators of functional state, physical development and physical fitness in the comprehensive assessment of the health of children with disabilities and SHN. A cross-sectiona; study was conducted in September 2025 at the boarding school for disabled children and children with SHN (n = 69) and the ordinary school (n = 69). Students aged 7−17 years were matched by gender, age, and body length. During the study we assessed physical development, psycho-functional state, physical fitness, and nutrition. The cluster analysis (k-means) was performed based on 11 indicators in a combined sample (n = 138). As a result, two clusters were allocated: “dysfunctional” (64 children, among them 35.9% from the ordinary school) with poor adaptation, excess body weight, high fat consumption; “functional” (74 children, among them 37.8% from the boarding school) with good adaptation, normal body weight, but low caloric intake. Contradictions have been identified between health groups and medical groups for physical education. The data obtained indicate that children with disabilities have various psycho-functional states that change during their stay in an educational organization, comparable in some cases to those of children from the ordinary school. It is recommended to supplement the comprehensive health assessment of children with disabilities and children with SHN by defining quantitative indicators of physical development, body’s functional state, and data on the children’s physical fitness. Furthermore, the child's lifestyle, typical for children of his/her age, should be taken into account.