The Wakatobi Islands are an archipelago of deep-sea islands lying off the south-east peninsula of Sulawesi. Despite being recognised as an Important Bird Area, the avifauna of these islands has long been neglected. While relatively extensive surveys have been carried out on nearby Buton Island (the largest satellite of South-east Sulawesi), the avifauna of the Wakatobi Islands went unstudied for nearly a century following the expedition of Heinrich Kühn in 1901-1902. Between 1999-2019 ornithologists visited nine of the archipelago's islands on eight expeditions, seeking to carry out a modern assessment of the islands' avifauna and re-evaluate the taxonomy of the avifauna. These expeditions combined transect surveys and mist netting. These formal surveys were targeted at small passerines, the focus of the taxonomic work, however all birds encountered were recorded allowing for a broad qualitative assessment of the avifaunal communities inhabiting the islands. In total, 100 bird species were recorded, of which 12 are Wallacean endemics, six are classified as Near Threatened and one as Critically Endangered. Here we present the species recorded during this study and review the historical literature to provide an inventory of the avifauna of the Wakatobi Islands. In addition, we review the taxonomy of Wakatobi populations including recent developments of note, highlighting potentially underappreciated endemism, and provide some information on relative abundance of bird species present.