The physiologically active lateral rootlets of all main trees in temperate forests are colonised by ectomycorrhizal fungi, forming so-called ectomycorrhizal. These symbiotic organs are the sites of exchange of nutrients, mainly P and N, provided from the fungal partner, and C from the host. Emerging from the ectomycorrhizas, fungal hyphae exploit the soil for the mobilisation and absorption of water and nutrient elements. By doing so, they connect the tree roots intimately with the soil and provide anchorage. The deposition of acidifying pollutants into forest ecosystems is a potential threat to the health and vitality of forest trees because it leads to the acidification and eutrophication of forest soils. Pollutants are also a threat to the functioning of ectomycorrhizas. Increased N concentrations in the soil lead to enhanced fungal N uptake and storage, and to enhanced N transfer to the host plants, and therefore to higher plant biomass of above ground parts. In consequence, there is a decrease of C allocation to the plant roots. This in turn leads to reduced ectomycorrhization, and to reduced production of external mycelia and fruiting bodies. Soil acidification leads to enhanced availability of AI, heavy metals, and radionuclides in the soil, all of which can be toxic to plants and fungi. Reduced growth of roots and hyphae are amongst the first symptoms. In ectomycorrhizas, the hyphae of the fungal tissues contain vacuolar polyphosphates which have the ability to bind AI, heavy metals, radionuclides and N. These electronegative polymers of phosphates represent an effective storage and detoxifying mechanism which otherwise is lacking in roots. Therefore, ectomycorrhizas have the potential to increase the tolerance of trees to acidifying pollutants and to the increased availability in the soil of toxic elements.