Plague and famine are two of the worst killers in human history. Both struck the Czech lands in the Middle Ages not long after each other (the famine of 1318 CE and the plague of 1348–1350 CE). The aim of our study was to try to relate the mass graves found in the vicinity of the Chapel of All Saints with an ossuary in the Kutná Hora–Sedlec site to these two specific events. For this purpose, we used stratigraphic and archaeological data, radiocarbon dating, and Bayesian modeling of 172 calibrated AMS ages obtained from teeth and bones of 86 individuals buried in the mass graves. Based on the stratigraphic and archaeological data, five mass graves were interpreted as famine graves and eight mass graves were interpreted as plague graves. Using these data and the calibration of the radiocarbon results of the tooth-bone pairs of each individual, we constructed the Bayesian model to interpret the remaining mass graves for which no contextual information was available (eight mass graves). In terms of Bayesian model results, the model fits stratigraphic data in 23 out of 34 cases and in all seven cases based on calibration data. To validate the model results on archaeologically and stratigraphically uninterpreted data, ancient DNA analysis is required to identify Yersinia pestis.