Based on the 2003-2019 electoral data, this article evaluates the level of pro-Europeanness in Czechia and Slovakia at the regional and sub-regional levels during and after their EU accession period. The TOPSIS multi-criteria evaluation method and cluster analysis were used to quantify the pro-European levels and to create the subsequent categories of territorial units. The results show support for the ideas of European integration primarily in large urban regions (Prague, Brno, Bratislava, Košice), territorial units with a higher concentration of ethnic minorities, larger scale agricultural activities (southwestern Slovakia), and a high degree of religiosity (northeastern Slovakia). The low level of pro-Europeanness was predominant in the less developed northwestern Czechia and parts of Moravia. In Slovakia, the Eurosceptic regions were mostly located in the northwest, where the values of statism, egalitarianism and nationalism have a strong tradition. This approach can be used to identify areas of weak support for the EU project at a spatially disaggregated level in other EU countries.