The article describes the results of work on the dual hygienic assessment of priority risk factors of the environment and the health condition of the population of Moscow. It is shown that in the territory of the metropolis the impact of conditions of negative factors on human health is retained. These trends are confirmed by the excess of the hygienic standards of pollutants in ambient air (up to 6.6 TLVc.e.), by the substantial increase (up to 65.8 %) of share of the centralized sources of water supply, water quality does not meet the hygienic standards due to the high level of non-standard samples of soil (more than 50 % on a number of sanitary-chemical and microbiological parameters in the territories of certain administrative districts). At the same time there is a tendency to a decrease in non-standard drinking water samples taken from the distribution network of centralized drinking water supply (from 4.36 % to 2.45 %). It was established that the primary morbidity have a number of positive trends to decrease, but exceeds the average indicators for individual classes and nosology, including the classes of "Respiratory diseases", "Diseases of the skin and subcutaneous tissue", "Neoplasms" and etc. by 4.1–68.3 %. Analysis of causality (about 50 significant biologically-based mathematical models were received) on the system of "quality of habitat (a risk factor) – health status (morbidity, mortality) " showed that the impact of negative environmental factors probably shape up to 29.2 ‰ of additional cases and up to 0.056 ‰ of the additional deaths per year. The largest contribution to the formation of the probability of additional cases is made by the excess of morbidity by hygienic standards of air quality and soil, mortality and air quality. Risk factors are phenol, benzo a pyrene, nitrogen dioxide, suspended solids, ammonia, chlorine and its compounds, and sulfur dioxide, etc., coming from the atmospheric air, and cadmium, microbiological agents, radioactive substances contained in the soil.