The development of agriculture in Slovakia in the last three decades has been influenced by two events: the transformation of agriculture after 1989 and Slovakia’s accession to the European Union in 2004. In this paper, we analyze the effects of Slovakia’s accession to the European Union on the development and structure of crop production. The aim of the paper was to identify connections, parallels and differences between the developments of the sown areas of the most important crops at the level of Slovakia and its regions in the period 2004–2020. Cluster analysis based on the similarity of the development of the sown areas divided the crops into four clusters (cereals; sugar-beet; oilseeds, multiannual fodder crops, maize; legumes, vegetables, potatoes). Multivariate analyses of the time series of sown areas also revealed similarities and differences between the regions of Slovakia. The results of the analysis point to regional differentiation and the identify two clusters. The first cluster comprises the Nitra and Trnava Regions, while the second cluster consists of the remaining six regions. The study has shown that changes in the agrarian sector after 2004, conditioned by Slovakia’s accession to the European Union, have been reflected in changes in the area and structure of cultivated crops, and in the differentiated development of sown areas.