It is through his book "Royal Commentaries of the Incas," and this source alone, that scholars from the 16th century onwards know the names and achievements of all the Inca Emperors all the way back to the founding Emperor or Sapa Inca, Manco Capac in 1100 AD.

His statements about the systematic murders of his male relatives on his mother's side are well attested to by other 16th century Spanish writers in South America. He tells us the Incas were not Native Americans, and that his cousin, Tupac Amaru, was both the last surviving male Inca, and the last Sapa Inca.

According to the Jesuite priest, Padre Blais Pascal, the Inca males were impossible to convert to Christianity and were therefore condemed to death by public execution where they were publicly garrotted in slow increments in an atempt get them to convert. This never worked as the Inca males believed since birth they were the living sons of the living Sun, their god.

Garcilaso accepted the Spanish notion that he was an "indian" until he reached the coast of Peru on his way to Spain, and saw the unclothed natives that were ruled by his mother's people and were also called Indians by the Spanish. By this time he was well into the writting of the second volume of his book and was appalled by the discovery that he and his mother's people were lumped together with these natives as "Indians". This prompted him to make the following revealing statement in the second volume of this book: "Just as I and my mother's people are not Spanish, I and my mother's people are not Indian." Queen Isabella recognized that Garcilso had oriental features and took great pains to ensure that he never encountered any envoys from that part of the world, fearing any contact between Garcilaso and an envoy from the orient might lead to oriental claims on the vast wealth that was comming out of Peru.

He describes how the Queshua people were formed out of the many subdued tribes and peoples, how they were deliberately intermingled to prevent a revolt against the Incas, and how they were given a common language, Queshua, which up until then belonged exclusively to the Aymara Natives. These peoples became collectively known by the language they spoke, their new common language, Queshua. After the Inca Empire broke up, the Queshua remained together as a loose federation of Queshua speaking peoples. This greatly confused the majority of modern Anthropologists, who never bothered reading 16th century history, making them believe it was the Queshua Federation that came together to form the Inca Empire in the first place.