The newly adopted Green Infrastructure Strategy is a key step in implementing targets of the European Biodiversity Strategy to 2020 (EBS). This study responds to policy needs for target 2 on ecosystems conditions and services, target 1 on implementing and enhancing coherence of the Natura 2000 network and sub-target 3b on integrating environmental concerns in forest management. Protected areas such as Natura 2000 sites form the backbone of Green Infrastructure. Their connectivity and integration in the unprotected landscape are essential to enable the movement and dispersal of species, to reduce the fragmentation of habitats and to render ecosystems more healthy and resilient. Connectivity of protected sites depends on the area of site, inter-site distances and landscape suitability (hostile and favourable land uses for species dispersal and movement). This report describes the JRC integrated model and derived results on the connectivity of Natura 2000 sites (only sites including forest). The model allows a harmonized, easily reproducible and automated EU wide assessment and comparison across countries. The Natura 2000 network is first characterised structurally in terms of simple (physically isolated) and complex sub-nets (spatially connected sites). Natura 2000 shares of complex sub-nets range from 40% in Bulgaria to 5% in Latvia. Second, the functional connectivity of the Natura 2000 subnets is addressed to tackle fragmentation by grey infrastructure including roads and intensive agriculture for species dispersing 500 m in average. A European-wide land use based friction map was created as a proxy of landscape suitability to measure functional (least-cost) distances between sub-nets. Functional connectivity was assessed according to two foci: one focused more on the area of subnets, another one on the inter-site landscape suitability and distances. The site area weighted index values ranges from 15 % (Denmark) to 78% (Malta). Best connected subnets with respect to inter-site landscape and distance were in Bulgaria, Belgium, Portugal, Ireland and Malta. High shares of functionally isolated subnets were in Greece, Denmark and Portugal. Functionally isolated sites and sites of key importance for connectivity were identified for two countries.