The Argentine Center-West was the southernmost portion of the Andes where domestication of plants and animals evolved. Populations located in the southern portion of this area displayed a hunter-gatherer subsistence economy up to historical times, and coexisted with farmers located to the north. Archaeological and biological evidence suggests that the transition to food production was associated with the consumption of a softer diet and a more sedentary way of life. This study tests the hypothesis that diet-related factors influenced morphological differentiation, by comparing functional cranial components of farmers and hunter-gatherers. Three-dimensional changes on eight minor functional components (anteroneural, midneural, posteroneural, otic, optic, respiratory, masticatory, and alveolar) were measured on skulls derived from both subareas. Volumetric and morphometric indices were calculated to estimate the absolute and relative size of components, respectively. Results of a paired t-test indicated that farmers have a smaller craniofacial size than hunter-gatherers. The components that varied the most were masticatory and posteroneural, showing smaller absolute and relative sizes in farmers. Discriminant analyses indicated that lengths and widths were the most affected dimensions of these and other components. The pattern of differentiation, which involves specific components, enabled us to exclude differential gene flow and stochastic mechanisms as the main causes. Instead, results support the hypothesis that diet-related factors associated with both subsistence economies influenced craniofacial morphology. A proportion of the observed variation associated with size differences can be explained by two systemic factors: the lesser quality of nutrition due to a low protein content in the diet, and a decrease of growth hormone circulation induced by a lower mobility due to sedentism. However, differentiation is better explained by a localized factor: the reduction in the masticatory and posteroneural components in farmers resulted from a decrease of masticatory stresses and workload on the head and neck, linked to the consumption of a softer diet. Am J Phys Anthropol, 2006. © 2006 Wiley-Liss, Inc.