New archaeological findings and the incorporation of new South American skull samples have raised fundamental questions for the classical theories of the Americas' settlement. The aim of this study was to estimate craniometric variability among several Asian and Native American populations in order to test goodness of fit of the data to different models of ancient population entries and dispersions into the New World. Our data set includes Howells' variables recorded on East Asian, North American, and South American natives (except for Na-Dene speakers). Five Fuego-Patagonian samples and one Paleoamerican sample were also included. A multivariate extension of the R-matrix method for quantitative traits was used to obtain Fst values, which were considered estimations of intergroup variation. Three main models for the peopling of the New World were represented in hypothetical design matrices. Matrix permutation tests were performed to quantify the fit of the observed data with 1) geographical separation of the samples and 2) three ways of settlement, which were the Three Migration Model (TMM), the Single Wave Migration model (SWM), and the Two Components Settlement Model (TCS). R-matrix results showed high levels of heterogeneity among Native Americans. Matrix permutation analyses suggested that the model involving high Amerindian heterogeneity and two different morphological patterns or components (derived “Mongoloid” vs. generalized “non-Mongoloid”) explains better the variation observed, even when the effects of geographical separation are removed. Whether these patterns arose as a result of two separate migration events or by local evolution from Paleoamericans to Amerindians remains unresolved. Am J Phys Anthropol 116:154–165, 2001. © 2001 Wiley-Liss, Inc.