This article is aimed at an analysis of operational subsidies on the Less Favoured Areas (LFA) in the European Union countries. With the help of cluster analysis, the EU countries were divided into groups and, using correlation and regression analyses, the relations between defined indicators were evaluate. The indicators of FADN EU related to the cultivated land area were completed with relative indicators. Some differences were proved in subsidy effectiveness between particular groups of the countries. The amount of operational subsidies only has a positive impact on subsidised costs in the mountain LFAs. Worse productive and climate conditions increase the dependence of the output on subsidies related to cost effectiveness. No dependence of the output share of subsidies and the subsidised costs was proven in all groups.