In paleopathology it is usually assumed that modern diagnostic criteria can be applied to infectious diseases in the past. However, as both the human species and populations of pathogenic microorganisms undergo evolutionary changes, this assumption is not always well-founded. To get valid estimates of the frequency (the point prevalence at death) of leprosy in skeletal samples, sensitivity, specificity, and sample frequency must be estimated simultaneously. It is shown that more than three symptoms must be evaluated in at least three samples in order to reach estimates with well-described properties. The method is applied to three skeletal samples from Medieval Denmark; the samples were scored for the presence of seven osteological conditions indicating leprosy. For the osteological conditions, sensitivity varied from 0.36–0.80, and specificity from 0.58–0.98. The frequency of leprosy in the three samples was: Odense (a lepers' institution), 0.98, 95% CI 0.64–1.00; Malmö (urban cemetery), 0.02, 95% CI 0.00–0.07; and Tirup (rural cemetery), 0.36, 95% CI 0.23–0.46. It is concluded that it is indeed possible to estimate disease frequencies without reference to modern standards, and that leprosy occurred with widely differing frequencies in different segments of the Medieval population in southern Scandinavia. Am J Phys Anthropol 115:380–387, 2001. © 2001 Wiley-Liss, Inc.