This article is concerned with the role of national governments in the rescaling of cross-border metropolitan governance structures in Europe. In the context of emergent cross-border metropolitan regions, the objective is to highlight the structuring effects of support policies to metropolitan areas at national level, in the context of their politics of scales, on the scalar configurations developed by local and regional actors. Using a comparative approach, the cases of Basel, Geneva and Luxembourg are singled out. The confrontation between German, Swiss and French state policies, and the modalities of the rescaling of levels of governance within the three cross-border metropolitan regions, allows us to underline the considerable influence of national guidelines on scalar reconfigurations. The structuring role of governments in this ‘new cross-border regionalism’ needs to be relativized, however, in functions of the specific characteristics of each context as well as factors relating to the actors involved.