The racial identity of Kennewick Man is at the heart of the controversy over his remains, but current research has called the very concept of race into question.

Some physical characteristics such as black hair are common among many, but not all, Native Americans. Others, including head and body shape, height, skin color, and facial hair, vary significantly. Native American men from Pacific Coast tribes, for example, often have heavy facial hair while other Native American men have none.

New research shows that the ancient Native American population was uniform, and that much of the variation seen by arriving Europeans was "made in America," the result of intermarriage and genetic changes among different groups over a long period of time.

Overall genetic variation among human groups is extremely small. This makes the study of small differences very important, and is why ancient human remains are measured and tested in an effort to learn more about how ancient groups might differ or be related. One such study was conducted in 1999 on Kennewick Man's body measurements. A comparison with a computer database of more than 300 human populations found "no matches" with any of them.

"The 'Caucasoid' Kennewick Man...has been the subject of extensive heated correspondence....To call it 'Caucasoid' is to connote aspects of ancestry, not simply morphology [form and structure]; it directly suggests that America was settled by Europeans and that those now called 'Native Americans' are actually less 'native' than they think. This is a strongly political statement requiring an exceptional level of validation....[The] 'racial' variation in cranial form of prehistoric Native Americans is well attested from earlier studies....Other material similar to Kennewick...also appearing 'Caucasoid' and with a very old date, nevertheless has mitochondrial DNA markers characteristic of American Indians, just as we should expect. So what is the point of racializing these remains? It serves only to clothe 21st-century issues like NAGPRA in the conceptual apparatus and vocabulary of the 19th century."
- Jonathan Marks, Physical Anthropologist, University of California at Berkeley, 1998

"Race does not exist. Racism does exist."
- Charles Keyes, Anthropologist, University of Washington, 1996

Modern research has shown that human populations cannot be divided into clearly defined, biologically distinct groups. Skull measurements, for example, vary widely not only within communities but even during a person's lifetime.

The old "three-race" model has been discarded by science, as has the idea that "racial" differences are linked to intelligence and behavior. Some noted scholars have suggested that the concept of race should be dropped altogether; others propose "ethnic group" as a more accurate term for human differences.

"Human populations are not unambiguous, clearly demarcated, biologically distinct groups. Evidence from the analysis of genetics (e.g., DNA) indicates that there is greater variation within racial groups than between them. These facts render any attempt to establish lines of division among biological populations both arbitrary and subjective."
- American Anthropological Association, 1998

The nineteenth-century idea that there are only three human races — Caucasoid, Mongoloid, and Negroid — emerged from European folk concepts of the Middle Ages about the significance of physical differences like skin color, head shape, or type of hair. All people were thought to belong to one of these races and most authorities believed that these physical differences also implied differences in intelligence, abilities, and general merit as human beings. Some believed that such "racial" differences justified social inferiority, colonial control, and even slavery. This attitude is illustrated by the following quote from the 1800s.

"The indominable, courageous, proud Indianin — how very different a light he stands by the side of the submissive, obsequious, imitative negro, or by the side of the tricky, cunning, and cowardly Mongolian! Are not these facts indications that the different races do not rank upon one level in nature?"
- Louis Agassiz, Professor of Geology and Zoology, Harvard University, 1850