The extent and type of instruments of the agricultural and structural policy of the European Union result from the postulate of an active role of government in the process of eliminating inefficiencies of market mechanisms within the concept of market failure. This concept suggests that in the realities of the market economy, the structure and size of supply is not reflected in adequate level of demand, as a result of the lack of autonomous re-balancing mechanisms. In practice, the processes of allocation of goods and services, despite the assumption of conditions of perfect competition and complete information as attributes of a complete market, show a number of disagreements. In accordance with some economists, intervention instruments have rather short-term effects at the macro level. In their opinion, if public funds do not reach the most efficient entities, the market in the long run will make corrections and efficiently allocate resources. Socio-economic transformations that took place in Poland in the period of EU membership caused a number of structural changes in the resources and distribution of production factors in agriculture. The main objective of the study is to analyse the some theoretical aspects concerning the concept of market failure and rationale for government intervention in the context of structural changes in agro-food sector and rural areas in Poland. The presented material includes analysis and assessment of CAP instruments influencing the production decisions of farmers, aspects of effectiveness and efficiency of EU financial support in regional development. In the last chapter the authors present conclusions related to the structural changes in agro-food sector, market imperfection and agricultural policy.