Several cranial-functional studies were made to compare the major (neurocranium and face) and minor (anteroneural, midneural, posteroneural, otic, optic, respiratory, masticatory, and alveolar) cranial components in different human populations. In the present study, samples from Paleoamericans and ancient and modern Amerindians from Valley of Mexico, Lagoa Santa, Tierra del Fuego Island, and Minas Gerais (Botocudos) were compared. The aim was to test the hypotheses that (1) “There are non-significant differences in the functional cranial components of different Paleoamerican crania, since they proceeded from a single dispersive effect” and that (2) “The biological variability of Paleoamerican and Amerindian functional cranial components was produced by random diversification evoked—after migration—by stochastic evolution”. Its acceptance will hold the criterion of temporal discontinuity between “megapopulations”, with a high incidence of migration and genetic drift. Its rejection will mean that Paleoamericans were not a morphologically homogeneous substratum, and that further populations could have—at least in part—originated from one or several central nuclei highly diversified by non-stochastic processes, like selection and adaptation. Multivariate (discriminant analysis and hierarchical clusters) were employed to get a general sample distribution. Univariate between-group standardized sD 2 distances were calculated to measure absolute and relative within-component differences. Statistical analyses were performed by the SYSTAT 9 program. Results lead us to reject both null hypotheses, suggesting that: (1) some cranial-functional differences were evident between both Paleoamerican samples, and (2) that several adaptative trends from Paleoamericans to modern Amerindians, and between Amerindians, might have occurred. It was concluded that adaptation could explain a fraction of the non-detectable cranial variation by the non-functional craniometric methods not explained by the “migration-drift” model for the American diversification.