The safety of baby foods is key to a child’s health, which, in turn, is one of the prioritized national goals. As they grow, children get exposed to numerous negative environmental impacts. Chemical contamination of baby foods can increase pediatric morbidity. The aim of this study was to investigate possible correlations between baby food contamination and primary pediatric morbidity using data on 65 Russian regions collected in 2012–2017 by the Russian Federal Information Public Health Surveillance Foundation. The data were processed in Microsoft Word 2010 and Microsoft Excel 2010. Of 67,940 samples of baby foods analyzed for chemical contamination, priority pollutants (toxic element) were detected in 14.1%. The most contaminated were fruit and vegetable purees (47.1%), followed by milk formulas and cultured dairy products (19.9%). We also analyzed 32,914 indicators of pediatric morbidity. The Pearson correlation analysis detected reliable correlations between baby food contamination and the primary incidence of endocrine disorders in infants, as well as the primary incidence of obesity, diabetes mellitus and cancer in children aged 0 to 14 years.