Hungarian agriculture experienced a particularly difficult period in the 1990s. In addition to problems related to changes in proprietorship, difficulties emerged in the field of production, foreign trade and the institutional system. The difficulties in agriculture also stimulated social tensions and further regional disparities to the disadvantage of agricultural areas. The transitional period has coincided with the EU accession negotiations and preparations for enlargement. After a brief discussion of the general situation and dilemmas in Hungarian agriculture, the paper seeks to summarize the difficulties of the agricultural sector in detail, as revealed during SAPARD (Special Accession Programme for Agriculture and Rural Development) programming at the micro-regional scale in two study areas.