Surveys of threatened lowland forest bird species and forest habitats were conducted during a 21-month census of lowland bird communities in Tambopata, Department of Madre de Dios, south-east Peru. A combination of distance sampling census methods and direct counts was used for the census in five sites located along the Rio Madre de Dios and Rio Tambopata. All five sites consisted of different forest types with significantly different habitat components. Three of these sites were classified as primary forest habitats whilst the remaining two were classified as disturbed forests. Population densities were calculated for eight of the threatened species recorded during the census. Density estimates of non-bamboo specialists were higher in primary forest habitats than in disturbed forest habitats. Density estimates of most bamboo specialists were higher in primary Old Floodplain forest with extensive bamboo understorey than in primary Middle/Upper Floodplain forest with smaller, patchy areas of bamboo understorey. Calculation of regional population estimates based on the amount of forest cover from satellite photographs shows that only two of the threatened bird species have substantial populations currently protected by the Parque Nacional Bahuaja-Sonene and Reservada Nacional de Tambopata. Selective logging operations that reduce overall tree biomass and remove a large proportion of palm tree species from primary forest habitats will have an adverse affect on local populations of four of the threatened bird species in the region.