The paper discusses the impact of the implementation of the EU Common Agricultural Policy on Czech agriculture with a special emphasis given to the effects resulting from the application of current direct payments system. Two approaches were applied: in an ex post analysis we address how accession have so far influenced structural changes income situation and production structure. Secondly, in an ex-ante analysis we apply the agent-based model AgriPoliS to simulate the impacts of decoupling top-ups on structural change and farm income. In the ex post analysis it has been observed that production decisions are strongly influenced by top-ups. Furthermore, the model shows that accession slows down structural change while decoupling of top-ups in 2009 will not lead to significant changes in farm restructuring nor income situation.