We report on the ornithological results of the first rapid biodiversity survey in the BX-044 polygon, one of the largest open vegetation enclaves in southern Amazonia, in the Brazilian states of Amazonas and Rondônia. Three-hundred and thirty species were recorded in all habitats surveyed, including closed (terra-firme, riparian, gallery, and campinarana forests) and open (cerrado and grassland) vegetation types. Over 90% (298) of all species were not shared between closed and open habitat types emphasizing the importance of inter-habitat diversity to the overall species richness recorded. Significant range extensions were documented for 34 species (30 of which were associated with the cerrado biome). Open vegetation enclaves contribute significantly to local avian species richness in Amazonia in addition to supporting species with special relevance to conservation with ranges centered in the cerrado, currently one of the most threatened biomes of South America. Conservation of Amazonian cerrado enclaves offers the unique opportunity to combine preservation of areas with high inter-habitat diversity with establishment of a complementary network of conservation units directed at preserving the cerrado biome throughout South America. Urgent steps must be taken to protect Amazonian open vegetation enclaves, which are still conspicuously under represented in the network of Brazilian conservation units, despite the fairly recent expansion of agriculture into these areas.