This paper discusses the concept of transnational innovation systems (TNIS) and presents some experiences in Europe in the formation of TNIS. The real cases show that supporting the emergence of Transnational Innovation Systems has clear benefits for the countries and the regions involved which may be related to the enlargement of consumer, labour and factor markets, enhanced competition, extended division of labour and increased specialization (Lundquist and Trippl, 2011: 3). Regional integration across borders can therefore be of high importance for small and emerging economies, where resources are scarce and markets are not large enough to support and stimulate innovation, like Central America. The paper concludes with some recommendations on how policy makers can facilitate the emergence and development of TNIS.