The present dissertation focuses on elucidating the role of cross-border cooperation (CBC) organisations in strategic interventions and development processes within a cross-border regional setting. CBC organisations’ role is analysed in the context of three interlinked theoretical concepts: multi-level governance, learning regions, and collaborative regional innovation. This approach makes it possible to analyse how institutionalised mechanisms like CBC organisations can enhance usage of complex tools and methods for the advancement of cross-border innovation. The research includes theoretical research, traditional empirical research including comparative international research of CBC organisations, and action research. The dissertation shows that a CBC organisation is a facilitator and an appropriate framework for fostering innovative and complex CBC forms and tools. The dissertation proposes institutionalised CBC models as mechanisms of intervention in regional policy and cooperation between different bordering countries considering the legal, organisational, financial, and functional dimensions of cooperation.