While the importance of individual protected areas (PAs) to biological conservation is widely acknowledged, rather few empirical studies have explicitly attempted to assess their ecological effectiveness. Significantly, this includes consideration of how well they represent the biodiversity of taxonomic groups for which the designation of these areas was not a primary or intentional goal. Here, we provide one of the most detailed comparisons to date of the avian biodiversity found inside and outside PAs, focusing on three PAs distributed widely across South Africa. Typically, bird assemblages were richer, with a higher density, and a different structural and functional composition inside than outside the PAs. Importantly, insectivore richness was much higher inside than outside, and the converse was true of granivores. Overall, these findings suggest that PAs do indeed provide valuable repositories for native biodiversity, with species richness, density and species composition being substantially different beyond their bounds. With human land-use increasing in South Africa, and habitat transformation recognized as a major and growing threat to biodiversity, such differences are expected to become greater.