The microstructural impact of diagenetic or post mortem alteration has been assessed in predominately human skeletal tissues. The method of assessment selected was microscopical analysis, mainly using backscattered electron imaging in a scanning electron microscope and, to a lesser extent, confocal reflection microscopy. The microstructural morphologies of post mortem alteration were investigated in archaeological material, both normal and pathological, from terrestrial and marine contexts. Further studies were undertaken on a case-by-case basis on skeletal material which offered some unique pathology, environmental context, spatial relationship, time variable, or mortuary practice. Additionally, the effect of diagenetic change on mitochondrial DNA (mtDNA) recovery and the potential location of DNA within the skeletal tissues were investigated. Two quantitative studies were undertaken to validate and measure the observed mineral density changes. The investigations showed that post mortem alteration or diagenetic change to skeletal material can be extensive, and can occur shortly after death. Diagenesis did not represent a post burial phenomenon as the term diagenesis suggests, but was found to have begun above ground in a range of exposural contexts. The implication of gut bacteria in the promotion of early bacterially-related microstructural change was strong, and it is proposed that body status at the point of, or soon after, death is important. Post mortem alteration to skeletal microstucture can provide environmental information, since terrestrial and marine contexts exhibited distinct morphologies. It may also provide localized environmental information within a stratigraphic matrix. Characterizing the post mortem microstructural and density changes to bone has helped to elucidate the preservational status of mtDNA in terms of its relative retrieval in archaeological specimens, and the potential location of mtDNA in bone. It is proposed that the shift in mineral density that was found in bacterially-remodelled specimens from terrestrial contexts, relative to the excellent preservation of marine specimens, may help to explain why marine vertebrates far outnumber terrestrial ones in the fossil record, since bacterially driven microstructural change is here considered to be a destructive form of fossilisation.