The main objective of the paper is to study the importance of regional preferences in financing agri-environmental programs. The analysis is based on results of a case study conducted in South-eastern Poland. As environmental protection in agriculture is complex and often considered in political strategies, it is worth analyzing the differences in perception of the respective environmental objectives from a regional perspective. Taking into account natural conditions and the economic situation in agriculture in the voivodship Podkarpackie, the question is, how regional objectives could be achieved effectively with a given budget. Using linear programming, we discuss in this paper, how regional preferences would guide budget allocation.