Based on spatial distribution maps for 495 breeding bird species inhabiting mainland Europe, we examined whether bird richness is well represented by the protected areas under the European Birds and Habitats Directives. The former regulates the designation of Special Protected Areas (SPAs) for birds, whereas the latter focuses on habitats through the Sites of Community Importance (SCI) and Special Areas of Conservation (SAC). All together, these areas conform the Natura 2000 network. To achieve our goal, we identified high-value richness areas by assessing the geographic distribution of all bird and important bird species (IBS, according to the Birds Directive) occurring in European Union (EU) countries, and investigated how well bird richness were represented in the current protected areas network. Our assessments showed little association between bird richness patterns and the cover of protected areas (PAs) across EU countries. The congruence between high-value richness areas of all bird species and IBS with PAs cover was moderate, suggesting that different conservation planning targets should be taken into account to safeguard IBS, or the composition of bird species. Our results also showed that 16 (3.9%) threatened species were present in gaps of PAs. The poor relationship between PAs cover and bird richness pattern found herein may provide evidence that the establishment of SPAs across Europe may not be fully accounting for richness patterns to enhance the performance of the current network.