In the context of demographic changes, the preservation of the health of all children, including those with health limitations, acquires particular importance. Children with health limitations are a special group that needs special conditions for effective education and upbringing. The comprehensive assessment of the health of such children lacks methodological uniformity because of poor communication between the bodies and agencies involved in assisting them, as well as insufficient harmonization of the applicable regulations. This study aimed to optimize the respective assessment process. The materials were medical records of students (n = 104), used as the sources of data. We revealed that children with health limitations tend to be ill often; the proportion of those developing normally in physical terms is low (57%); most of the children with abnormal physical development (20%) are short. The recommendation is to use two methods for assessing children's physical development: regression coefficients, which describe growth disorders, and body mass index (BMI), which reports the degree of excess body weight. We identified faults in the results of the comprehensive health assessment: 68 children belonging to the 5th health group were qualified for the preparatory physical education group, which creates a high risk of a severe clinical situation in a physical education lesson. From the perspective of optimization of the comprehensive assessment of the condition of children with health limitations, the recommendation is to make the wording of the Order of the Ministry of Health of the Russian Federation more clear and to harmonize it with the conceptual framework of the Orders of the Ministry of Labour and Social Affairs of the Russian Federation.