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The Rio Pandeiros is a left bank tributary of the Rio Sao Francisco, rising in the north of the state of Minas Gerais, in southeastern Brazil. This region lies in an ecotone between three ecoregions: Cerrado (the prevailing vegetation type), Caatinga and Atlantic Dry Forests, ensuring a high diversity of habitat types. Here we report our observations conducted in the region during the last nine years. We recorded 315 bird species. The avifauna is typical of the Cerrado, but several species typical of the Caatinga or deciduous forests also occur in the region. The large marsh along the river’s lower course harboured many waterbirds, but contrary to our expectations, no breeding colonies of waterbirds were found in the area. Several threatened or poorly known species were found, such as Laterallus exilis, Nyctiprogne vielliardi, Phylloscartes roquettei and Knipolegus franciscanus. Comments on biogeography and conservation are also presented.