All over Europe, but especially in post-communist countries, the institutional environment has been undergoing major changes. In Slovakia, regaining their autonomy has led local governments on the path of fragmentation, unsustainably high expenditures for the provision of public services, and an increase in transaction costs. Current policies targeting these issues are heavily focused on intermunicipal cooperation (IMC). Based on four case studies of different institutional arrangements, this paper aims to investigate which endogenous political, institutional, cultural, and geographic factors influence cooperation among Slovak municipalities. Through the application of social network analysis and regression analysis, we reached several relevant conclusions. A number of common assumptions were confirmed, namely that population size and heterogeneity play a major role, but also that the impact of political affiliation as a deciding factor of IMC is not as straightforward as previous evidence suggested. Results also underline the importance of cross-sectoral partnerships such as the EU’s LEADER initiative as a viable alternative to more traditional forms of IMC (but with some limitations).