A number of studies based on linguistic, dental and genetic data have propo
sed that the colonization of the New World took place in three separate wav
es of migration from North-East Asia. Recently, other studies have suggeste
d that only one major migration occurred. It is the aim of this study to as
sess these opposing migration hypotheses using molecular-typed HLA class II
alleles to compare the relationships between linguistic and genetic data i
n contemporary Native American populations. Our results suggest that gene f
low and genetic drift have been important factors in shaping the genetic la
ndscape of Native American populations. We report significant correlations
between genetic and geographical distances in Native American and East Asia
n populations. In contrast, a less clear-cut relationship seems to exist be
tween genetic distances and linguistic affiliation. In particular, the clos
e genetic relationship of the neighbouring Na-Dene Athabaskans and Amerindi
an Salishans suggests that geography is the more important factor. Overall,
our results are most congruent with the single migration model.