Physical development is the most important indicator of the health of children and adolescents, since it enables monitoring thereof. This study aimed to assess the harmonicity of physical development in schoolchildren living in the new territories of the Russian Federation. We used the anthropometric data (body length and weight) of schoolchildren aged 7 to 17 years from the Donetsk People's Republic (DPR; 4004 people) and the Kherson region (2902 people). More than 60% of schoolchildren from the DPR had harmonious physical development, and the least number of harmoniously developed children was observed in the age groups of 11−14 years (58.4% of boys and 56.6% of girls); as for the Kherson region, the physical development was harmonious in more than 50% of schoolchildren therefrom, and lowest number of harmoniously developed children was found in the age groups of 11−14 years (43.1% boys and 45.3% of girls). We identified significant differences in the appearance of the relative risk of disharmonious physical development between boys aged 7−10 and 11−14 years in the DPR and the Kherson region (χ2 = 21.6, p < 0.001 and χ2 = 59.328, p < 0.001, respectively), as well as between girls of the same age groups (χ2 = 14.383, p < 0.001 and χ2 = 11.843, p < 0.001). These relative risk figures indicate that there is a direct link between the territories and the likelihood of disharmonious physical development. The correlation analysis and the calculation of relative risk yielded determination of the critical groups among schoolchildren aged 11−14 in which the number of children developed disharmoniously was the largest.