Past studies have revealed that much of human craniometric variation follows a neutral model of population relationships. At the same time, there is evidence for the influence of natural selection in having shaped some global diversity in craniometrics. In order to partition these effects, and to explore other potential population-specific influences, this article analyzes residuals of craniometric distances from a geographically based neutral model of population structure. W.W. Howells' global craniometric data set was used for these analyses, consisting of 57 measurements for 22 populations around the world, excluding Polynesia and Micronesia because of the relatively recent settlement of these regions. Phenotypic and geographic distances were derived between all pairs of populations. Three-dimensional multidimensional scaling configurations were obtained for both distance matrices, and compared using a Procrustes rotation method to show which populations do not fit the geographic model. This analysis revealed three major deviations: the Buriat, Greenland Inuit, and Peru. The deviations of the Buriat and Greenland Inuit appear to be related to long-term adaptation to cold environments. The Peruvian sample is more similar to other New World populations than expected based on geographic distance alone. This deviation likely reflects the evolutionarily recent movement of human populations into South America, such that these populations are further from genetic equilibrium. This same pattern is seen in South American populations in a comparative analysis of classical genetic markers, but not in a comparative analysis of STR loci, perhaps reflecting the higher mutation rate for the latter. Am J Phys Anthropol, 2010. © 2009 Wiley-Liss, Inc.