The sea and inland hinterland of Baltic Europe form a unique macro-regional unit. Strong collaboration links, and competition in the Baltic Sea region, are an inherent feature of the region from the beginning of its civilization development. Since 2004, the Baltic Sea has become an internal sea of the European Union. This fact no doubt strengthened the cooperation of the countries in the region. In many spheres, these ties take the form of networking. The EU Strategy for the Baltic Sea Region is an important stimulus for further integrations. The objective of the article is to identify changing trends and the structural transformation in the Baltic integration process instigated by the implementation of this strategy. The document contains common goals, which strengthen cooperation and draw on the Baltic Sea potential. Three main pillars are outlined in the Strategy: marine protection, better interconnection of the region and growing prosperity. The essence of cooperation involves joint development plans on various levels: governmental, regional and local with the participation of research institutions, regional cooperation infrastructure, operational programmes, as well as the private sector. Political stabilisation and economic development may transform, in a longer time span, the emerging transnational Baltic Europe into a new economic and cultural European centre. The choice of research methodology applied in the study derives from the nature of collected data, i.e. literature regarding scientific accomplishments in the Baltic cooperation, analysis of working documents and reports drawn up by public institutions, the European Commission, and EU national and regional strategic documents.