Negative environmental factors (chemical, physical, biological) may cause significant negative influence both over environment and the health of the population. Maximal number of sources of negative impact is located in industrial regions. Factors and existing methods of the estimation of ecological risks of urban territories are discussed. The main steps of estimation of ecological risks of urban territories are described. New approaches to estimation of ecological risks of urban territories are suggested. Program provision has been developed for the estimation of ecological risks allowing to forecast the level of pollutions of the environment of urban territories. The results of approbation of the new method and program provision of estimation of ecological risks on the example of the territory of Samara region of Russia have been described.