Traditionally, anthropometric method is used in clinical practice for the diagnosis of excess body weight. Obesity is the excess development of primarily visceral and subcutaneous adipose tissue, which can be diagnosed by bioimpedance analysis (BIA). The study was aimed to assess the role of BIA of body composition in the diagnosis of the physical development disorders in children and adolescents. Anthropometric assessment and BIA were performed in 431 Samara school students aged 12–16 of the health status groups I and II (230 boys and 201 girls). The results were analyzed with the use of the regional regression scores, BAZ indices, and the body fat percentage values. The results of estimation using the regression scores showed that 22.61% of boys and 23.43% of girls were overweight, while more than 2/3 of the sample had a normal pattern of physical development. The BAZ indices revealed a significantly higher proportion of overweight children among boys (25.7%), than among girls (11.5%, p < 0.01). The body fat percentage fluctuations based on the BIA data were found not only in children with disharmonious physical development, but also in 60% of children with normal body weight. Moreover, the data of BIA confirmed the body weight fluctuations, revealed with the use of the regression scores, in the significantly larger number of cases compared to the low body weight and excess body weight, diagnosed based on the BAZ indices. Accordingly, anthropometric analysis with the use of the regional regression scores may be used at the baseline for the early diagnosis of the nutritional status disorders in children. To confirm overweight and obesity in children, as well as to provide further treatment, the reliable method for estimation of the body fat content is required, which may be the method of BIA.