The consequences of urbanization, such as increased exposure to pathogens, have long been considered detrimental to human health. During the first half of the Danish medieval period, towns were established and throughout the period population increased. The following study analyzes the relationship between urbanization and disease frequency – specifically leprosy and tuberculosis – in four skeletal samples from medieval Denmark using a paleoepidemiological approach. Skeletons from two urban sites (Ole Wormsgade and Ribe Grey Friary) and two rural sites (Øm Kloster and Sejet), all located in the Jutland region of Denmark, were selected for this analysis (n = 204). All skeletons included date to the middle part of the Danish medieval period (AD 1200-1400). Six skeletal leprosy indicators and six skeletal tuberculosis indicators were analyzed, and disease frequencies in the samples were estimated using a probabilistic approach based on lesion sensitivity and specificity. The effect of tuberculosis on survival in urban and rural samples was evaluated using Kaplan-Meier survival analyses. The frequency of leprosy at death varied between four and 19 percent among the four cemeteries with Ole Wormsgade having the highest frequency. The estimated frequency of tuberculosis at death varied between 39 and 69 percent. Here, Sejet cemetery had the highest frequency. There were significant differences in survival for those with and without tuberculosis-related lesions between sites, but there were no significant differences between urban and rural sites. The analyses presented in this paper suggest that disease prevalence in skeletal samples cannot be sufficiently explained by urbanization alone; rather, there are likely other biological and behavioral sources of heterogeneity that are contributing factors to past disease experience.