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Animal domestication led to changes in the interaction between animals and humans, including new ways of exploitation, which could potentially leave lesions on the animals' bones. This study aims to examine changes in the prevalence of pathological manifestation following changes in human‐animal interactions as a result their domestication. For this purpose, we studied 19,565 animal remains recovered from archaeological excavations, dated from the Pre‐Pottery Neolithic period to historical periods and assigned the pathologies into types. Of these, 60 animal remains presented pathological lesions. The suspected pathological cases were validated using a microscope, X‐ray, and/or micro‐CT scan. Lesions were divided into four categories: trauma, aging/musculoskeletal stress marks (MSM), periodontal diseases, and inflammatory processes. Then, our database was combined with previously published data to a total of 26,596 animal remains, out of which 128 demonstrated pathological lesions. We found that the prevalence of lesions in animals was higher in the historical periods compared with prehistoric periods. Moreover, based on a comparison between recent gazelles living in captivity and those living in the wild, we found that captivity resulted in the deterioration of the animals' health. We concluded that pathologies were more frequent in livestock in historic periods, in comparison with wild species and livestock from earlier periods. Such lesions were common not only in working livestock (cattle and donkeys) but also in non‐working domesticates (caprines and chickens) and companion animals (dogs and cats). Variations in the pathological frequencies between these three categories may be attributed to differences in exploitation, including the intensification of farming and herding. Finally, this study provides a unique reference dataset for zooarchaeologists when studying ancient animal assemblages. [ABSTRACT FROM AUTHOR]