The origins of the ancient Egyptian state and its formation have received much attention through analysis of mortuary contexts, skeletal material, and trade. Genetic diversity was analyzed by studying craniometric variation within a series of six time-successive Egyptian populations in order to investigate the evidence for migration over the period of the development of social hierarchy and the Egyptian state. Craniometric variation, based upon 16 measurements, was assessed through principal components analysis, discriminant function analysis, and Mahalanobis D(2) matrix computation. Spatial and temporal relationships were assessed by Mantel and Partial Mantel tests. The results indicate overall population continuity over the Predynastic and early Dynastic, and high levels of genetic heterogeneity, thereby suggesting that state formation occurred as a mainly indigenous process. Nevertheless, significant differences were found in morphology between both geographically-pooled and cemetery-specific temporal groups, indicating that some migration occurred along the Egyptian Nile Valley over the periods studied.