This study aimed to evaluate the possible use of mercury as a medical treatment at the medieval monastic hospital Skriðuklaustur (ad 1494–1554) in eastern Iceland. The individuals excavated from Skriðuklaustur exhibited a wide range of pathological conditions, including the only skeletal evidence of venereal syphilis in Iceland. Skeletal remains from the Skeljastaðir cemetery (ca. ad 1000–1104) in southern Iceland were also analysed in light of the site's proximity to the mercury emitting volcano Hekla. The eruption produced a severe toxic fallout resulting in the mass mortality of livestock and is believed to have caused the abandonment of Skeljastaðir and the other farms in the region. The skeletal analyses and sampling were conducted according to standard anthropological methods. Mercury concentrations were determined in human (n = 50), faunal (n = 23), and soil (n = 22) samples using inductively coupled plasma mass spectrometry. Individuals from both sites exhibited elevated mercury concentrations. At Skriðuklaustur, some individuals showed normal concentrations, but those with pathological conditions (e.g., hydatidosis, syphilis, tuberculosis, and other non‐specific infections) had the highest concentrations overall. On the other hand, all the individuals analysed from Skeljastaðir exhibited elevated mercury concentrations, some of which were remarkably high. A few of the individuals buried at Skeljastaðir post‐date the eruption, possibly indicating that some of them experienced heavy exposure to volcanic emissions. The less extreme concentrations at Skriðuklaustur may be a result of attention to dosage and the temporary nature of mercurial treatments. None of the faunal and soil samples presented with concentrations exceeding the normal limit, implying that diagenesis was not a concern in this research. The conclusion is that a variety of factors from medical treatment to scholarly work lead to mercury exposure at Skriðuklaustur, whereas at Skeljastaðir, volcanogenic emissions are implicated.