Within many institutional collections are skeletal and mummified human remains representing a part of our species’ adaptation and evolution to various biocultural environments. Archaeologically recovered individuals come from deep into our past, and possess information that provides insight into population history, genetics, diet, health and other questions relevant to all living peoples. Academic concerns have been raised regarding the reinterment of these collections due to the rise of the international repatriation movement, the passage of various laws and implementation of institutional policies. While all potential research questions cannot be anticipated, the proactive documentation of collections is one way to ensure primary data are maintained for future study. This paper explores developments in digitization technology that allow the archive of virtual copies of human remains, and an example of how anatomical and archaeological collections can be digitized towards pragmatic research goals. The anatomical variability of the human atlanto-occipital (AO) articular surfaces was studied using non-metric categorical shape, 2D measurement and 3D morphometric analyses to provide reference standards for the reassociation of individuals from commingled skeletal remains, such as found in some archaeological sites or forensic investigations including mass grave or mass disaster recovery scenes. Results suggest that qualitative shape observations and caliper-derived measurements of the articulating AO condyles tend to display significant sexual dimorphism and biological ancestry-related size and shape differences. Variables derived from a scanned 3D mesh, such as condylar angle and articular surface curvature, quantify biomechanical variation and display a stronger congruency within individuals. It is recommended that a two-stage approach involving initial screening and identification of possible reassociation candidates is accomplished with a linear osteometric approach, followed by 3D laser scanning of the candidate joint surfaces for morphometric analyses to confirm reassociations when destructive DNA typing is not allowed or otherwise impractical due to cost or other resource restrictions.