Institutional cross-border interactions support the EU goals for regional development by creating joint local initiatives and cross-border institutional cooperation networks. This paper aims to develop a new methodological strategy for studying the processes of cross-border territorial integration within the EU. By building on the Cross-Border Institutional Thickness (CBIT) conceptual framework, the paper analyses the policy targets in the cross-border regional context. The CBIT measures how its components support the required development or policy goals in different regions. Therefore, this paper provides a theoretical and methodological approaches to the CBIT model and contributes to future studies in this field.