The data-set described here comprises cranial pathology data and cranial age assessment for 113 individuals from four Mesolithic-Neolithic sites in the Danube Gorges, Serbia. Calibrated radiocarbon dates by archaeological site were included where available. The data were collected after anthropological analysis of this collection. This dataset is available from UCL Discovery in .csv format. The reuse potential of these data is great for paleoepidemiology studies, and for associated time-series analyses in this region and beyond. Furthermore, these data can be used for comparative studies of cranial pathology and aging profiles in other Mesolithic-Neolithic collections.