Identifying endemic species and the areas of endemism delimited by them is central to biogeography. However, the impact of distinct taxonomic approaches on these patterns is often neglected. We investigated how three different taxonomic approaches impact the patterns of bird endemism in the Cerrado. The first two approaches (at species and subspecies levels) were based on traditional taxonomy based on the biological species concept. The third approach was based on a revised alternative taxonomy that sought to identify evolutionarily significant units (ESUs). In this third approach, after identifying the endemic taxa using traditional taxonomy, we revised their validity, removing biologically meaningless entities. We then detected the areas of endemism delimited by these endemic taxa under the three taxonomic approaches. We found that traditional taxonomy at the species level underestimated bird endemism by ignoring some ESUs that were considered subspecies. In contrast, traditional taxonomy at the subspecies level overestimated bird endemism, leading to the recognition of spurious areas of endemism because several of the purported endemic subspecies were taxonomic artefacts. The revised taxonomy provided a more refined picture of patterns of avian endemism in the Cerrado, suggesting that the use of ESUs improves the results of biogeographical analysis.