The change in subsistence strategy, from hunting and gathering to agriculture, and the associated development of social hierarchy form a series of changes of particular biological interest. There are two main aspects to these changes, which interact and modify each other; the first relates to human biology and human variation, and the second to the history of population movements along the Nile. The emergence of Egyptian civilisation was preceded by the introduction of agriculture in the Nile Valley. The emergence of the First Dynasty was a major development in the political and sociocultural transformation of the agricultural communities inhabiting the lower Nile Valley. Human variation can act in terms of differing responses to diet and ecology, and can be recognised through trends in biological markers. This study has employed biological measures to ascertain the pattern of biological changes occurring in the Nile Valley through the Predynastic and Early Dynastic periods. A model was developed both to predict the pattern of physical changes expected to affect the individuals and to link these biological changes with the genetic structure of the local population. The first portion of the study concentrates on understanding the population affinities of the skeletal groups studied. These results suggest the local population continuity exists in Egyptian populations, but that there is also some evidence of changes in population structure, which may reflect immigration and admixture of new groups. The next sections of the study consider the actual biological effects of this migration, intensification of agriculture and the formation of the Egyptian state on the anatomy of the local population. Changes in growth outcome were found, with the differences being of a greater magnitude among the males than the females. These changes were associated with changes in the expression of cranial robusticity within the populations. Increasing levels of dental disease were found through time. The model developed in the study was therefore modified to explain the differences in expression of physical traits in males and females. The biological results were then linked with archaeological evidence to better understand the role of social ranking on human skeletal biology.