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This paper aims to present the first evidence of animal diseases from the Central Balkan Eneolithic, a prehistoric period that lasted about 2000 years. The eponymous site of Bubanj in south‐eastern Serbia provided a diachronic perspective on animal pathologies developing during this long time period. We analyzed 71 animal remains showing evidence of pathological changes. All of the remains exhibiting anomalies were subjected to macroscopic analysis, while the specimens with the most prominent alterations also underwent X‐ray and CT imaging. Anomalies were observed mostly in domestic animals. Only in caprines were all of the different types of anomalies present, with dental pathologies being the most frequent. Degenerative bone alterations were noted in around 78% of the domestic cattle specimens, while congenital anomalies were the most common type in domestic pigs. Pathological changes were also noted in dogs, aurochs, red deer, wild boars, beavers, and bears. In most cases, the anomalies were caused by hereditary and environmental factors. Caprine dental pathologies were the result of aging and poor‐quality nutrition. In domestic cattle, besides being caused by environmental factors, the degenerative alterations might also have been work related. The lack of paleopathological data from other Eneolithic sites in the region, and the scarce or non‐existent evidence from the previous (Neolithic) and succeeding (Bronze Age) periods prevented comparative analyses and discussion of the results within wider temporal and spatial frames. Establishing a paleopathological investigation of animal remains with anomalies from the prehistoric Central Balkans should be a standard, in order to provide us with a better understanding of human–animal interactions.

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