Objectives of this dissertation thesis are evaluation of the effect of application of commercial ectomycorrhizal inocula, laboratory-prepared fungal inocula, growth substrates on growth, ectomycorrhizal colonization of roots, ectomycorrhizal diversity and content of macroelements in assimilation organs of Norway spruce (Pica abies [L.] Karst.) and Scots pine (Pinus sylvestris L.) during several growing seasons after sowing. Also, estimation of the effect of the method of planting stock cultivation, growth substrates on growth, ectomycorrhizal colonization, ectomycorrhizal diversity of European beech (Fagus sylvatica L.) during several growing seasons after sowing. The work contributes to knowledge about effect of used ectomycorrhizal inocula, growing substrates and method of planting stock cultivation. The experiments were established on two sites in glasshouse located on the campus of Tuzvo and in the area of the nursery centre Jochy. The experiments were in complete randomized block design with three repetitions. Experimental unit in Borovica 2017, Smrek 2018, Smrek 2019 experiments was PVC container with seedlings of each combination of the main effect. In Smrek 2014 experiment was experimental unit a nursery bed. In Buk 2018 experiment were experimental unit’s nursery bed and container. Despite the results of experiments presented in this study are valid just for used planting stock in a given growth conditions and cannot be generalized, but several outputs can be emphasized and any also indicate possibilities of their practical use. In the Smrek 2014 experiment, a significant effect of the growth substrate on biometric parameters, relative abundance of ectomycorrhizal morphotypes was observed even after transplanting. The inoculation at the start of the experiment affected only the relative abundance of 1 morphotype after transplanting. In the Borovica 2017 experiment, a significant effect of the growth substrate on biometric parameters was observed only in the 1st growing season. Inoculation significantly affected the relative abundance of only 1 morphotype during the experiment and the values of diversity indices in the 1st growing season. In the Smrek 2018 experiment, a significant influence of the growth substrate on the morphology of the root system after the 1st vegetation period and on biometric parameters, relative abundance of morphotypes, ectomycorrhizal colonization after the 2nd vegetation period was observed. Inoculation significantly affected biometric parameters, relative abundance of morphotypes, and ectomycorrhizal colonization over the course of the experiment. Inoculation also affected root morphological parameters and diversity indices after the 1st growing season. In the Buk 2018 experiment, seedlings growing in peat substrates achieved significantly higher values of biometric parameters than in mineral soil. On the contrary, significantly higher values of relative abundance of morphotypes, ectomycorrhizal colonization and diversity indices were in mineral soil. Container seedlingss had significantly higher biometric parameters. Barerooted seedlings from the bed reached significantly higher values of relative abundance of morphotypes, ectomycorrhizal colonization and diversity indices during the experiment. In the Smrek 2019 experiment, only 1 morphotype was distinguished, which was significantly more represented on seedlings inoculated with mineral soil. Ectomycorrhizal colonization with other inocula was non-existent.