Presented here are results of analyses of excavated skeletal material from the early modern period in Tartu, Estonia, for evidence of syphilis. Our understanding of the incidence of syphilis in Estonia, and the causes of its spread, are discussed. All of the skeletal samples that were positively identified for syphilis included evidence of bone lesions on the cranium. Percentages of remains with signs indicative of syphilis were found at a rate of 0.50%, which accords with a figure of 0.77% from Britain for the same period. Evidence presented suggests that syphilis was a problem not only in the metropolitan area of Tallinn, but also in the less populous cities of Estonia. It is concluded, given that the excavation sites represent different dates from the period, that syphilis was a significant health problem in early modern Tartu.