The article describes the organizational structure and results of the implementation of a unique interdepartmental system of targeted health care and disease prevention in risk groups of the most vulnerable categories of the population (children and pregnant women) resided in industry-affected areas, which is an integral part of the regional system of the management chemical risks for population health. The system is represented by a modular stepwise principle of taking a set of science-based hygienic, health care and disease prevention measures and includes hygienic diagnostics and multimedia health risk assessment; environmental epidemiology studies; biological monitoring of toxicants; evaluation of the personal multimedia toxic burden in the most vulnerable population groups; biological disease prevention, clinical and laboratory diagnostics and rehabilitation treatment of diseases, informing population about health risks posed by chemical contamination of the environment and measures of risk elimination and prevention; performance evaluation including a cost-benefit analysis. The system health management has been implemented since 2001 in 17 municipalities of the Sverdlovsk Region with the mean annual coverage of 11,000 preschool children, pregnants and women of childbearing age. In 75-80% of enrolled children, clinical and diagnostic indices improved, thus indicates to the health promotion: morbidity rate in these children decreased by 30-40%, disease frequency and duration became 2-4 times lower, and over 80 additional incident cases per 1,000 children were prevented. In 2005-2016, the prevented economic damage to public health exceeded two billion rubles. Since 2009, the system has been applied in the Republic of North Ossetia-Alania (the town of Vladikavkaz), the Orenburg Region (the towns of Mednogorsk and Gay), and the Krasnoyarsk Krai (the city of Krasnoyarsk).