Setting aside protected areas is widely recognized as one of the most effective measures to prevent species from extinction. Accordingly, there has been a tremendous effort by governments worldwide to establish protected areas, resulting in over 100,000 sites, which are set aside, to achieve the 10% target proposed at the Fourth World Park Congress in 1992 in Caracas. The main effort of the European to achieve this target is the Natura 2000 network of protected areas, comprising over 25,000 sites representing 18 % of the area of the 27 Member States of the European Union. The designation of Natura 2000 sites was based on species and habitats listed in the Annexes of the Habitats and Birds Directive. The effectiveness of the selection process and the resulting Natura 2000 network has often been questioned as each country made its designations largely independently and in most cases without considering the theories of optimal reserve site selection. However, the effectiveness of the selection process and the Natura 2000 network has never been explicitly analysed at the European scale. Here we present such an analysis focusing on the representation of Annex II species of the Habitats Directive in the Natura 2000 network relative to a random allocation of species to sites. Our results show that the network is effective in covering target species and minimizing the number of gap species (i.e. species not represented in a single site of the Natura 2000 network). We demonstrate that the representation is uneven among species. Some species are overrepresented and many species are only represented in a low number of sites. We show that this is mainly due to differing patterns in species ranges, as wide-spread species are inevitably represented in many sites, but narrow ranged species are often covered only by a small number of sites in a particular area. Finally, we propose a representation index that detects species that are underrepresented and could be used to direct future conservation efforts.