Intergovernmental relations (IGR) have become increasingly salient in many Western States, adding (or redefining) a new dimension of politics within multi-tiered domestic arenas. Different institutional tools for managing transformed intergovernmental relations (Intergovernmental Arrangements) are both theoretically possible and empirically observable. In this paper, the consequences of varieties in Intergovernmental Arrangements are investigated in two neo-regional countries – Italy and Spain – in one of the public policy sectors most affected by the processes of territorial re-scaling: health care. Grounded on a new-institutional perspective and based on the adoption of a Most Similar System research Design (MSSD), the comparative analysis explores whether observable differences in IGAs can account for variations in intergovernmental policy-making processes channelled through them, particularly in terms of the kind of conflict lines and actors’ coalitions emerging in IGR processes. Overall, collected evidence shows that, once set in place, differently organized Intergovernmental Arrangements are able to play a part in shaping the politics of intergovernmental relations.