Background/Purpose: In the context of the European Biodiversity policy, the Green Infrastructure Strategy is one supporting tool to mitigate fragmentation, inter-alia to increase the spatial and functional connectivity between protected and unprotected areas. The Joint Research Centre has developed an integrated model to provide a macro-scale set of indices to evaluate the connectivity of the Natura 2000 network, which forms the backbone of a Green Infrastructure for Europe. The model allows a wide assessment and comparison to be performed across countries in terms of structural (spatially connected or isolated sites) and functional connectivity (least-cost distances between sites influenced by distribution, distance and land cover). Main conclusion: The Natura 2000 network in Europe shows differences among countries in terms of the sizes and numbers of sites, their distribution as well as distances between sites. Connectivity has been assessed on the basis of a 500 m average inter-site distance, roads and intensive land use as barrier effects as well as the presence of "green" corridors. In all countries the Natura 2000 network is mostly made of sites which are not physically connected. Highest functional connectivity values are found for Spain, Slovakia, Romania and Bulgaria. The more natural landscape in Sweden and Finland does not result in high inter-site network connectivity due to large inter-site distances. The distribution of subnets with respect to roads explains the higher share of isolated subnets in Portugal than in Belgium.