地位未定
The exact taxonomic placement of the lesser yellow-headed vulture and the remaining six species of New World vultures remains unclear. Although both are similar in appearance and have similar ecological roles, the New World and Old World vultures evolved from different ancestors in different parts of the world. Just how different the two are is currently under debate, with some earlier authorities suggesting that the New World vultures are more closely related to storks. More recent authorities maintain their overall position in the order Falconiformes along with the Old World vultures or place them in their own order, Cathartiformes. The South American Classification Committee has removed the New World vultures from Ciconiiformes and instead placed them in "Incertae sedis", but notes that a move to Falconiformes or Cathartiformes is possible. Like other New World vultures, the lesser yellow-headed vulture has a diploid chromosome number of 80.