The aim of this study is to verify the hypothesis that structural genotypes exist in EU agriculture. To verify the hypothesis, Eurostat data from the 2010 and 2016 Farm Structure Survey for 258 NUTS 2 regions were used. 21 structural variables were calculated on the basis of the data and then they were used to carry out a latent profile analysis. At the last stage of the research, the influence of structural genotypes on the productivity of production factors was verified using the MANOVA method. The obtained results confirm the existence of 5 structural genotypes: (1) small farms and a polarized agrarian structure, (2) very small, non-specialized, labour-intensive farms and a polarized agrarian structure, (3) large farms and non-polarized agrarian structure, (4) average farms, (5) very large farms – outliers. What differed the most among farms was the concentration of production. Additionally, the relative stability of the adherence of the regions to a given genotype was confirmed, as well as the influence of this relation on the productivity, in particular on labour productivity. Any transitions between clusters concerned, in the vast majority, those regions where the scale of production was higher.