Studies of ectomycorrhizal fungal communities in forest soils are usually restricted to the uppermost organic horizons. Boreal forest podzols are highly stratified and little is known about the vertical distribution of ectomycorrhizal communities in the underlying mineral horizons. Ectomycorrhizal root tips were sampled from seven horizons in three continuous columns of a 52-cm deep podzol profile. Root tips were sorted into morphological groups and the colonising fungi identified by sequencing of the rDNA ITS region. The vertical distribution of mycorrhizal taxa was examined. A relationship between ectomycorrhizal species composition and soil horizon was found. Tomentellopsis submollis , three Piloderma species and Dermocybe spp. were found predominantly in the upper horizons while Suillus luteus , Lactarius utilis and three undescribed Piloderma species were associated with the mineral horizons. Two thirds of the root tips were found in the mineral soil and half of the taxa were restricted to the mineral horizons. The results highlight the need to include the mineral soil in order to gain a more accurate representation of the ectomycorrhizal community.