The growing incidence of nutrient-related diseases is a global challenge. The aim of this work was to study consumption of staple food products and to estimate the incidence of nutrient-related diseases in Voronezh region. Food consumption was analyzed from the reports of the local branch of the Federal State Statistics collected over two 5-year periods (1995–1999 and 2012–2016). The incidence of nutrient-related diseases was estimated based on the reports providing information about patients’ visits to healthcare facilities. The districts of Voronezh region were assigned to 5 ranks. Over the studied periods, the population of Voronezh region considerably changed its diet: consumption of fish and seafood, fresh fruits, meat, vegetables, gourds and melons, eggs, vegetable oil, milk and dairy products per person increased significantly. At the same time, consumption of sugar, breads and potatoes still exceeds the recommended intake 1.42-2.04-fold, which means that the main component of the diet is carbohydrates. We observed a significant 4.5-fold increase in obesity incidence, a 1.8-2.0-fold increase in the incidence of anemia and endocrine disorders and a 1.2 increase in the incidence of gastrointestinal diseases. In terms of prevention measures, the priority should be given to areas at a high risk of nutrient-related diseases.