The Philippine islands hold a concentration of species diversity and endemism of global importance, yet few studies have analyzed biogeographic patterns or attempted to prioritize areas for conservation within the archipelago. We analyzed distributions of 386 species on 28 Philippine islands and island groups, documenting intense concentration of species richness, especially of endemic species, on the two largest islands, Mindanao and Luzon. Factors identified as influencing species richness included island area, maximum elevation, and Pleistocene patterns of connection and isolation. Reserve systems were developed based on heuristic complementarity algorithms, and compared with the existing Integrated Protected Areas (IPAS) system in the country, showing that IPAS is an impressive first step towards protecting avian diversity in the country. Addition of presently proposed reserves on Palawan and Mindoro would make IPAS a near-optimal reserve design, at least at the level of island representation. Important challenges remain, however, with regard to design of reserve systems within islands to represent complete island avifaunas.