This study deals with an effect of fertilization on amount and quality of free amino acids in soil from wet meadows affected by nutrient loading. Free amino acids were analysed in the soil from the field experiment situated at wet meadows, where an increased nutrient input is simulated (fertilizer NPK). The experiment was established on two sites with different types of soil {--} Záblatí with organic soil and Hamr with mineral soil, both areas in the South Bohemia region. The soil was repeatedly sampled for more than two years and year. One part of this study is focused on testing of ninhydrine-method and HPLC-method for measuring free amino acids and efficiency of different extractants.