In this study, we compare the craniofacial morphology of four Sumidouro skulls and one Lund skull of paleo South Americans from Lagoa Santa, Brazil, with worldwide prehistoric and recent human craniofacial metric data, and suggest an alternative view of the migration history of early South America. Affiliations of samples and individuals were examined by the principal coordinate plot generated by Relethford and Blangero's R-matrix method, the neighbor-joining method based on genetic distance generated from the same R-matrix, and Mahalanobis distances and typicality probabilities. For these analyses, we examined certain variables claimed to have been influenced by the environment, such as maximum cranial length and maximum cranial breadth. Although the number of craniometric variables seems to influence the results of the analysis, it appeared to not obscure the ancestral and descendant relationships and regional kin relationships greatly in the instance of this study. Using Howells' worldwide comparative dataset but without the Jomon sample, previous research had suggested that Brazilian Paleoamericans, the Lagoa Santa, were probably closely related to Australian Aborigines and Africans as opposed to Native Americans and Northeast Asians. On the other hand, using multivariate statistics, our results show that Lagoa Santa individuals exhibit stronger morphological affinities with the prehistoric Jomon of Japan, archaic Americans of Indian Knoll Kentucky, Windover Florida, and Tennessee, and recent Tierra del Fuegans of South America, than with the Melanesians and Australians. Moreover, Jomon, Lagoa Santa, and archaic North Americans all display close relationships and ties to each other. This suggests that the early inhabitants of South America were probably not related to Australo-Melanesians, but rather to the Late Pleistocene descendants of Northeast Asians such as the Jomon. Also, they are related to the archaic North American populations and recent Central and South Americans.