Although processes of cranial modification have been documented throughout the world, the effects on craniofacial landmarks are poorly understood. Such understanding is needed to assist the further understanding of craniofacial morphology and dysmorphology and in the interpretation of craniometric studies assessing issues of biological distance. Samples of both clinically normal and modified crania recovered from the same archeological site in Peru were studied using a three-dimensional approach to evaluate differences in landmark location. The crania were associated with the Ancón site from the central coast, corresponding to the Late Intermediate period (ad 900-1300). Analysis revealed that vault modification had no significant effect on the locations of landmarks of the facial and basal regions. As expected, differences were found on some landmarks of the cranial vault.