Teeth are often the preferred source material for isotopic and genetic assay involving ancient biomolecules. The assumption is that dental tissue preserves better due to its anatomically protected location, the enamel cap, and lower porosity compared to bone. However, this assumption has not been widely tested. Some similarities in diagenetic processes are to be expected due to similarities in structure and chemical composition of dentine and bone. This has led to the suggestion that bone can be used as an indicator of dental preservation, as a pre-screening technique in the selection of suitable samples for biomolecular studies. Thus, direct testing of the correlation between bone and tooth preservation and diagenesis is needed. This paper reports the results of the histological characterization of diagenetic alterations within 25 human femur-tooth pairs, from a Medieval to modern (AD 1850) cemetery in Eindhoven, the Netherlands. The results showed that teeth do indeed preserve better overall, but not always, and that this was dependent on the main diagenetic factor(s) at the burial location. Furthermore, good correlations are found between the microstructural preservation of bone and teeth; similar processes of decay were observed within bone and teeth of the same individual. Overall, the study demonstrated that histological analysis of bone is useful for the identification of degradation processes that affect biomolecular preservation in skeletal material. In this way, sample selection and analytical strategies can be optimized.