The Inca civilization was an ancient civilization in South America on Earth. They, like many other civilizations, were inspired by the Exxilons. (NA: The Left-Handed Hummingbird)
When the Great Bairn landed on Earth, it was found by the Incans. They built the Tomb of the Bear around it. When the Doctor believed the Great Bairn was in danger, he stole it from the tomb in 1934 and delivered it to David Kershaw in 2009. (WC: Snowfall)
In the Doctor's TARDIS there was an Incan quipu. (NA: Sanctuary)
The Doctor once met the Cybermen in an Incan temple. (VG: The Mazes of Time)