Andean civilization probably began c. 9500 BP. Based in the highlands of Peru, an area now referred to as the punas, the ancestors of the Incas probably began as a nomadic herding people. Geographical conditions resulted in a distinctive physical development characterized by a small stature and stocky build. Men averaged 1.57 m (5'2") and women averaged 1.45 m (4'9"). Because of the high altitudes, they had unique lung developments with almost one third greater capacity than other humans. The Incas had slower heart rates, blood volume of about 2 l (four pints) more than other humans, and double the amount of hemoglobin which transfers oxygen from the lungs to the rest of the body.

Archaeologists have found traces of permanent habitation as high as 5,300 m (17,000 ft) above sea level in the temperate zone of the high altiplanos. While the Conquistadors may have been a little taller, the Inca surely had the advantage of coping with the extraordinary altitude. It seems that civilizations in this area before the Inca have left no written record, and therefore the Inca seem to appear from nowhere, but the Inca were a product of the past. They borrowed architecture, ceramics, and their empire-state government from previous cultures.

In the Lake Titikaka region, Tiwanaku is recognized by Andean scholars as one of the most important precursors to the Inca Empire, flourishing as the ritual and administrative capital of a major state power for approximately 500 years