Agriculture of the Czech Republic has features of submonate and montane agriculture. More than half of the surface of the Czech Republic are less favourable areas (LFA). Active state support of farming focused on the extensive production and maintenance of the countryside and the other environmental services is the crucial point of a successful development of competitive and economical (from the point of view of the environment) production in LFA. Organic farming is carried out on the area of 6 % of the surface of agricultural land, most of agricultural land is worked with conventional methods of farming. In the Czech Republic there are significant differences between structure of the organic and conventional farming, especially in the share of arable land and share of permanent grasslands. The differences between organic and conventional farming systems can be located also in structure of production and in some other parameters (average acreage of the farms…). The contemporary state of farming has been evaluated and organic and conventional farming systems have been compared in the framework of the analysis of structure of farming in the Czech Republic. The selective group of 437 associations was divided into three different subgroups, and into several categories according to the farming method and altitude. Parameters of plant and animal production and use of the agroenvironmental programmes and measures are evaluated. The evaluation of the structure of farming permits to find optimal possibilities of future development of conventional and organic farming in the Czech Republic and of arrangements of the settings of grants and subsidies