This paper discusses the Slovak regional economy structural changes, development and factors of regional economic specialisation and geographic concentration of sectors with a focus on agriculture from 1995 to 2012. Specialization and sector geographic concentration were quantified by Herfindahl and Entropy indices. At the national level we found steadily growing share of crop production at the expense of animal production. Regional concentration of both, crop and animal production and animal production specialisation has been increasing. Spatial clusters of similar specialised regions were detected for crop production. Linear panel models were used to estimate the effect of selected factors on regional crop and animal production specialisation. The agricultural policy instruments, including the CAP had significant effect on regional crop and animal production specialisation patterns. Provision of the complementary national direct payments (CNDP) and investment support had positive effect on regional crop production diversification. Density of regional road network, average annual temperature in the growing season, average annual rainfall in the growing season and provision of the LFA payments had positive effect on both regional crop and animal production diversification.