The Natura 2000 Network represents the greatest step forward yet in conservation in Europe, although its effectiveness is sometimes questioned, especially in Mediterranean regions. Bats are protected by the Habitat Directive and the presence of certain species is a prerequisite before Special Areas Conservation (SAC sites) can be included as such in the Natura 2000 Network. However, the effectiveness of SAC sites as regards the protection they offer to bats, especially cave-dwelling species, remains to be evaluated. We assess the effectiveness of the SAC system for protecting the roosts of six species of cave-dwelling bats and for protecting suitable and optimal habitats, using ecological niche models. Gap analyses indicate that c. 60% of roosts are protected by SAC sites, with values ranging from 45.8% for Miniopterus schreibersii to 72.2% for Rhinolophus hipposideros. The protection offered to suitable and optimal habitats was found to be much lower in general, with values of below 40% in all cases. Our results emphasize the potential value of non-natural caves (e.g. mines and buildings) for the conservation of bat populations, and the importance of assessing the efficiency of protected areas by considering distribution models that incorporate different types of information (e.g. roosts and use habitat) concerning species occurrence.