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In order to evaluate the impact of atmospheric pollutants emitted by the industrial settlement of Milazzo (Italy) on agriculture, sulphur dioxide and ozone levels in air were monitored and the data were used to estimate yield losses of the most widespread cultures. Trace element concentrations in crops and soils were also detected and metabolic profiles of soil microbial communities were considered. Vibrio fischeri test was used to appraise airborne pollutant ecotoxicity and epidemiological studies on causes of death distribution were carried out to characterize health state of people living in the area. All the sampling points were selected in farms on the basis of a theoretical meteo-diffusive model of industrial air pollutants. Experimental SO2 and O3 values mainly exceeded the threshold established by Italian and EU regulations to protect vegetation and they correspond to estimated significant crop losses. Conversely toxic element residues in soils and in agroalimentary products were generally lower than the fixed values. SO2 and O3 concentrations, toxic element contents and ecotoxicity levels of airborne pollutants were not related only to industrial site emissions, while the fluctuations on metabolic profiles of soil microbial communities seem to agree with the predicted deposition of xenobiotic compounds from the industrial plants. The epidemiological study evidenced a better health state of populations living in the investigated area than in the Messina province and the Sicily region but, inside the area, males living in the municipalities closest to the industrial settlement exhibited a worst health state than those in the very far ones.