Formed by three Andean ranges and two peripheral elements, the complex mountainous system of Colombia harbours a diverse avifauna (>1,500 spp.) characterized by high large-scale beta diversity and endemism. In these mountains there are 25 protected areas covering c. 3.5 million hectares but not all ecosystems are adequately represented. We conducted an analysis of representation of bird species in these protected areas for eight subregions of the Colombian mountains by means of a comparison between potential and recorded faunas in each area. Potential faunas were compiled by considering the distribution of species across the subregions, their elevational ranges, and the elevational extent covered by each protected area in each subregion. Analyses were performed separately for all species and for migrant species, with an emphasis on threatened species. Bird inventories are lacking for nine of the protected areas. Existing inventories have representation values of 4–91% for all species, and 3–72% for migrant species. Assuming that all potential species occur within protected areas, representation values for the subregions were high (74–100%) but may be as low as 26% when representation values are estimated using recorded species only. For most Andean subregions representation decreased with decreasing elevation, revealing a lack of protected areas at lower elevations. In addition, 31 threatened species (26% of total), which mainly occur at lower elevations and in adjacent lowlands, are not covered by protected areas. Thus, although birds are relatively well protected by the system of reserves in the mountains of Colombia, significant gaps remain, particularly for threatened species.