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The article describes a new scientific and methodological approach to designing geographic information systems of health and environmental monitoring for urban areas. Geographic information systems (GIS) are analytical tools of the regional health and environmental monitoring; they are used for an integrated assessment of the environmental status of a large industrial centre or a part of it. The authors analyse the environmental situation in Voronezh, a major industrial city, located in the Central Black Earth Region with a population of more than 1 million people. The proposed research methodology is based on modern approaches to the assessment of health risks caused by adverse environmental conditions. The research work was implemented using a GIS and multicriteria probabilistic and statistical evaluation to identify cause-and-effect links, a combination of action and reaction, in the dichotomy "environmental factors - public health". The analysis of the obtained statistical data confirmed an increase in childhood diseases in some areas of the city. Environmentally induced diseases include congenital malformations, tumors, endocrine and urogenital pathologies. The main factors having an adverse impact on health are emissions of carcinogens into the atmosphere and the negative impact of transport on the environment. The authors identify and characterize environmentally vulnerable parts of the city and developed principles of creating an automated system of health monitoring and control of environmental risks. The article offers a number of measures aimed at the reduction of environmental risks, better protection of public health and a more efficient environmental monitoring.