Mercury and lead were present in European medieval society in very different ways. Mercury was rare and occurred only as point sources such as medicine, the colour pigment cinnabar and in the process of gilding. Lead was ubiquitous in the urban societies and present even in the rural ones; the main source was lead glazed kitchenware. We have investigated the distribution of both elements in the bones of rural and urban populations in Northern Germany and Southern Denmark. 283 individuals from six different medieval cemeteries have been studied. The individuals have been examined anthropologically to determine sex and age at death, while samples of the cortical and trabecular bone tissues from the femur have been analysed chemically. Prior to chemical analyses the samples were thoroughly decontaminated. The samples were measured for mercury, lead and calcium. From the data of the rural populations we have established limits for the background exposure levels: 80 and 300 ng g− 1 for mercury and 5 and 7 μg g− 1 for lead in cortical and trabecular bone tissue respectively. On average 21% of the population was exposed to Hg above background, but the frequency of high Hg exposure varied from cemetery to cemetery. Lead exposure reached even out into the rural communities where ca. 35% of the population was exposed above background. No correlation was seen between Hg and the proposed social status indicator Pb. Based on measurements of calcium we propose for the first time a criterion for rejecting the analysis of a skeletal sample due to contamination.