Innovative high-tech small and medium sized enterprises (SMEs) are thought to be drivers of economic renewal and growth. However, due to their limited size, SMEs face two fundamental innovation barriers: the risk that other organizations appropriate the returns to the newly created knowledge by SMEs (knowledge leakage), and a lack of understanding and recognition of their business on the part of potential stakeholders (legitimacy deficits). Based on a panel study of 196 SMEs this paper shows that biotech, ICT and clean tech firms choose different strategies to deal with knowledge leakage and legitimacy deficits. To prevent knowledge leakage, high-tech SMEs are very selective in choosing their R&D partners and collaborate with basic rather than applied technology developers. Furthermore, to gain organizational legitimacy, high-tech SMEs pursue activities that focus not only on product development but also on generating awareness and understanding of their technologies.