Most critical discussions of European immigration policies are centered around the concept of Fortress Europe and understand the concept of the border as a way of sealing off unwanted immigration movements. However, ethnographic studies such as our own multi-sited field research in South-east Europe clearly show that borders are daily being crossed by migrants. These findings point to the shortcomings of the Fortress metaphor. By bringing to the fore the agency of migrants in the conceptualization of borders, we propose to understand how borders are being shaped by taking as a starting point the struggles of mobility. Against the background of our two-year transdisciplinary research project TRANSIT MIGRATION European migration and border policies cannot be longer conceptualized as being simply oriented towards the prevention of migration. Since migrants cross the borders daily, what happens if the borders' permeability is part of the way they work? If so, we have to investigate the mechanisms of border policies and practices anew. One is the concept of the border or migration regime. The other is the concept of the autonomy of migration. Our concept of ethnographic regime analyses is based on a transdisciplinary approach, comprising political studies, anthropology and sociology.