The objective of this study has been to follow modifications in the content of Cu, Zn and Mn in the topmost layer of soil which had been fertilized for many years with farmyard manure and mineral fertilizers or with mineral fertilizers alone. Soil samples were collected in 2002-2005 from a trial established in 1986 on proper brown podsolic soil, according to the random block design with four replication. The first factor consisted of organic fertilization (manure applied every two years or without manure). The second factor involved different rates of mineral fertilization. Rates of nutrients in the mineral fertilizers were identical in both experimental series – with or without manure. In each year, the same crop was grown on both fields, in a crop rotation system: sugar beet (2002), spring barley (2003), maize (2004) and spring wheat (2005). Plant available forms of nutrients were extracted from soil in 1 mol HCl dm-3 solution. After extraction, the content of metals was determined by atomic absorption spectrophotometry. The results underwent statistical processing using analysis of variance for a two-factor experiment. The content of available forms of copper, zinc and manganese in soil regularly amended with manure was evidently higher than analogous concentrations determined in soil receiving only mineral fertilization since 1986. Manure most strongly improved the concentration of Cu (nearly 1.7-fold), while producing the weakest influence on manganese (over 1.3-fold more). In absolute values, however, the increase in availability of manganese was the highest, reaching on average 52 mg kg-1 of soil. Differentiated mineral fertilization with nitrogen or potassium as well as manganese and liming to a lesser extent than manure modified the availability of Cu, Zn and Mn in soil. Among these nutrients, nitrogen most often increased the content of plant assimilable forms of metals in soil, which may have been caused by its acidifying influence.