The importance of the rainforests on the island of São Tomé for biodiversity is well known. However, the area only recently received full legal protection as a National Park and currently few resources are available to enforce that legislation. With rapid economic development forecast for the island, active conservation efforts are essential. Here we study the distribution and density of the island's endemic bird species, including nine that are Globally Threatened, within the National Park. Sites, covering the full range of primary forest types, were surveyed using distance sampling methods. No introduced species were observed. The highest number of species, including eight Globally Threatened species, were found in lowland rainforest, although many were infrequently encountered. Higher altitude sites were less diverse, but supported some of the common endemic species at extremely high densities. The least diverse assemblage, with generally lower species population densities, occurred at the most accessible mid-altitude forest site. Distance from settlements was a key explanatory variable for the presence of all Globally Threatened species, indicating that human habitation has negative effects on the suitability of nearby forest habitats. This suggests that, as infrastructure improvements proceed, populations of endangered species will come under growing pressure. Integrating the needs of biodiversity conservation and development represents a major challenge for many biodiverse countries and on São Tomé, as elsewhere, may best be achieved by preserving the still intact functioning forest ecosystem.