This paper deals with the migration of Cu, F, Hg, Mn, P, Pb, Zn, U in brown and podzol soil profiles of Southeast Estonia. The aim of the study was to find out why the soils in Southeast Estonia are poor in almost all elements – whether they are carried out from the humus horizon or the parent material of soil is initially poor in them. The mean contents of the elements studied are 1.2–1.7 times lower as compared with Estonian mean contents; only Hg has a mean content similar to the Estonian mean. To solve this problem, the contents of the above-mentioned microelements were analysed in the humus horizon and parent material in brown and all podzol soils. Analysis of the migration of elements shows that Cu, Mn, P, Pb, Zn are relatively sedentary in soil profile. The content of F and U in the humus horizon is twice lower than in parent material, while Hg content in the humus horizon is twice as high. Briefly: the main reason for the lack of nutrient microelements in brown and podzol soils in Southeast Estonia is their low content in parent material; carrying out from the humus horizon is less important.