One-year-old seedlings of silver birch (Betula pendula Roth.) were grown in pots filled with a soil substrate that originated from an area polluted by a phosphate fertiliser factory and characterised by a high soil Al level and low Ca/Al ratio or with a substrate from an area regarded as free from toxic pollution. In addition the effect of fertilisation with a mixture of nutrients was evaluated. Birch seedlings grew slowest in the unfertilised polluted substrate. In the unfertilised polluted substrate seedlings were characterised by high biomass allocation to roots (60% vs. 30 to 40% in control or fertilised substrate), lower diversity of ectomycorrhizae and the lowest rate of root and substrate microbial respiration. Roots of seedlings grown in the polluted soil were characterised by a significantly higher level of phenolic compounds. Fertilisation of plants grown in the polluted soil accelerated their growth, and lowered RWR (g root g-1 plant) and increased biomass allocated to foliage. Our results indicate that elimination of air pollution does not decrease the toxic effect of a polluted soil. Fertilisation may improve the condition of seedlings growing in polluted soil, however it was not able to eliminate entirely the adverse effect of soil pollution.