Skeletal samples from pre-Colonial Peru and Bolivia, dating from AD 300 to 1450, were sampled and analyzed for lead content using a non-destructive X-ray fluorescence (XRF) technique. A total of 99 lead measurements were made on bones recovered from three regions of the Southern Andes. Predominantly trabecular bones demonstrated clearly higher lead concentrations than predominantly cortical bones. The magnitudes of lead concentrations and the differences between bony areas that are predominantly cortical and those that are trabecular, indicate diagenesis as the major contributor to observed lead levels. Diagenetic contributions of lead are less substantial in cortical bone. Soil sample analyses confirmed significant quantities of lead in the sediments. Repeated measurements of a tibia and femur from a single individual suggest that the cortical shafts of these bones have similar susceptibilities to lead diagenesis. This is significant for designing alternative sampling strategies in areas where preservation is poor and a specific bone may not be present in all individuals. The XRF system used in this study demonstrates an improved precision of measurement compared with previously reported applications.