Concentrations of Cd, Pb, Zn, Ca, Sr, Al, Fe, Ti, Fe and Mn were determined in bone samples from human skeletons dating back to the Late Medieval Period from Pianosa Island (Grosseto, Italy) and to the Eneolithic (i.e. the Copper Age) from the Lunigiana region (municipality of Cassola, Massa Carrara, Italy), in order to obtain insights into diet, heavy metal contamination and differences in accumulation between humerus and femur. The influence of diagenetic processes, which alter archaeological remains within their burial environment, was evaluated by multivariate statistical analysis, comparing trace element concentrations both in bone and in soil still present in the humerus and femur. This method and Sr:Ca and Zn:Ca ratios provided reliable information on diagenetic processes and diet in the two periods and enabled assessment of accumulation of heavy metals (Cd, Cu, Pb).The results indicate that diagenesis did not influence concentrations of Pb, Cu, Zn, Ca or Sr, and that there was no significant difference in accumulation of these elements between humerus and femur. Sr:Ca and Zn:Ca ratios indicated vastly different diets in the two periods. The occurrence of high levels of Cu (1368.64 mg/kg d.w.) in a humerus from the Copper Age sample possibly due to exposure during copper smelting, was a very interesting outcome.