Currently, the tri-national border area between Germany, Czech Republic and Poland is characterised by low level of transnational cooperation between science and SMEs, as an own investigation of the Saxon-Bohemian border area proved (Krause-Jüttler et al. 2014). The reasons are to find in structurally, socially and historically determined factors. National differences induce a mismatch and therefore an opacity of administrative structures and relevant stakeholders. This hinders the emergence of transnational linkages. At once, the whole border area is distinguished by micro-enterprises, that possess only a low level of innovation capacity in terms of human and financial resources for innovation projects as well as an unincisive project management to execute transnational research collaborations. Existing funding instruments to support transnational linkages between science and business currently are not being adapted to their needs and low financial capacity. Social respectively cultural causes for the marginal occurrence of linkages are to find in a rather poor level of cooperation climate which can be described by an absence of trust and thus missing openness for transnational cooperation within companies and research organisations. Moreover, language barriers and a deficit of knowledge respectively an underestimation of potential cultural differences continue to play an important role regarding the inexistence of transnational linkages. The status quo causes, that remarkable capabilities for the integration of different national competencies in order to develop innovations remain unutilised.