Extensive research in human genetics on presumably neutral loci has shown that the overwhelming majority of human diversity is found among individuals within local populations. Previous apportionments of craniometric diversity are similar to these genetic apportionments, implying that interregionally differing selection pressures have played a limited role in producing contemporary human cranial diversity. Here we show that when cranial variation is independently partitioned using principal components analysis of Mosimann shape variables, some estimates of interregional craniometric differentiation are larger than those for most genetic loci. These estimates are similar to estimates for genetic loci where interregionally differing selection pressures are implicated in producing the observed patterns of variation within and among regions. These results suggest that differences among regions in at least some cranial features, particularly in the nasal region, are in part the product of interregionally differing selection pressures. Moreover, these results have implications for assessing the biological affinities of prehistoric samples that are temporally separated from contemporary human reference populations. Am J Phys Anthropol 124:000–000, 2004. © 2004 Wiley-Liss, Inc.