The article deals with comparison of agricultural subsidies in the member states of the EU in the period 2004-2012 based on the database Farm Accountancy Data Network (FADN). During the monitored period we found a slight increase of operational subsidies with the fact that variability shows a decreasing trend. In the structure of subsidies we can see a clear transition to payments separated from production with significant differences between original member states and new member states (NMS). With the help of cluster analysis the member states were divided into groups according to their operational subsidies, total production and costs. With the use of correlation analysis we assessed the relationships between production, costs and operational subsidies re-counted per ha of utilised agricultural area. The increase of subsidies will not occur in higher cost productivity and only very slightly will it occur in the higher share of subsidized costs.