The Bolivian highlands, permanently settled for at least 21,000 years, were part of the culture of Andean South America before the arrival of the Spaniards. The records are fragmentary but suggest that agriculture started about 3000 B.C. and that the production of metal, especially copper, began 1,500 years later.

By 600 B.C., the first great Andean empire had emerged on the high plateau between the mountains known as the Altiplano. This empire, the Tiahuanacan, was centered near the southeastern side of Lake Titicaca and included urban centers around the lake, as well as enclaves in different ecological zones from the eastern valleys to the Pacific Coast. Tiahuanaco was a great center of trade and religion, and the impact of its culture spread far beyond the boundaries of present-day Bolivia. Apparently, the Tiahuanacan Empire was established through colonization rather than through conquest. Its rapid expansion after 1000 and sudden collapse around 1200 are still poorly understood.

The collapse of Tiahuanacan influence resulted in the rise of seven regional kingdoms of the Aymara, the most powerful states located in the densely populated area around Lake Titicaca. The Aymara, a belligerent people who lived in fortified hilltop towns, had an extraordinary ability to adapt to the unique climatic conditions of the region and increased their food supply through irrigation and the process of freezing and drying crops. By maintaining colonists in the semitropical valleys on the eastern slopes of the Andes and on the Pacific Coast, they were able to produce both tropical and highland crops.

The Aymara completely dominated the Uru, another major ethnic group in the pre-Columbian southern Andes. Although the Uru might have preceded the Aymara in the region, by the twelfth century they were poor fishermen and landless workers.

The Aymara, however, were not able to contain the expansion of the Quechua, the third major ethnic group. After the collapse of the Tiahuanacan Empire, a Quechua-speaking state emerged in the area around Cuzco (in present-day Peru). In the early fifteenth century, the Quechua, who became known as the Incas when they adopted the name of their rulers, were the most powerful group in the northern highlands. As the Aymara kingdoms in the south became weaker in the second half of the fifteenth century, the Incas began to conquer them.

The Bolivian highlands became known as the Kollasuyo, a densely populated area with great economic and mineral wealth that constituted one of the four administrative units of the Inca Empire. The highest official of the Kollasuyo was responsible only to the Inca (the emperor) and supervised a group of provincial governors, who in turn controlled members of the Aymara nobility. Under a draft system called the mita, the Incas forced local Indians in the Kollasuyo to work in the mines or on construction projects or to serve in the armies, compensating them fully for their labor. Despite their goal of extreme centralization, the Incas did not fundamentally change the organization of the Aymara kingdoms, which remained relatively autonomous. Many local chiefs kept many of their former powers and were, in general, reinforced by Inca authority. They were also able to retain their culture, their local religion, and their language. The regional nobility, although forced to send their children to Cuzco for education, continued to hold private property. Moreover, the system of sending colonists to the eastern valleys and the coast was tolerated under Inca rule.

In 1470, however, several Aymara kingdoms rebelled against Inca rule. The Incas completely defeated two states and pacified the region by sending mitimas, Quechua-speaking colonists, to Aymara territory, especially to the southern valleys and to the more central valley regions where Cochabamba and Sucre were later founded. By the beginning of the sixteenth century, the Incas had fully established their rule over the Kollasuyo. In the 1980s, the legacy of this resettlement policy could be seen in the predominance of Quechua speakers in many areas of Bolivia.

The Incas failed, however, to conquer the nomadic tribes in the eastern Bolivian lowlands. The remains of Incan fortresses there are evidence of this failure and suggest that the Incas could subdue only those cultures that were primarily based on agriculture. Thus, the Indian groups of the eastern two-thirds of Bolivia preserved their ways of life to a great extent, even after the Spanish conquest.