A special part of archaeology, so-called archaeozoopathology or veterinary paleopathology is dedicated to studies of paleopathological changes in animal remains and contributes to the knowledge of ancient veterinary medicine and the history of diseases. In our study, we analyze paleopathological changes determined by gross observation and diagnostic imaging in the animal material originating from eight archaeological sites in Croatia. A standard archaeozoological analysis was carried out and specimens with visually detected macrostructural changes were radiographed. In total, 50 animal remains with altered macrostructure were identified in the archaeozoological material excavated from 2010 to 2022 at eight archaeological sites in Croatia. According to the taxonomic analysis, most of the bones with macrostructural changes originated from cattle (N = 27, 54% of the total number of bones with macrostructural changes), followed by the bones of small ruminants (N = 12, 24%) and pigs (N = 8, 16%). The horse, carnivore and chicken were represented with one bone each (2%). Radiological examination showed that three samples (6%) had a regular bone macrostructure, i.e., no pathological changes were visible upon radiological examination. The majority (64%) of pathologically altered bones are a consequence of keeping/working, followed by traumatic causes (20%). Changes in the oral cavity were found in 10% of specimens. Our study showed that gross examination will continue to be the primary method for the identification of pathologically altered remains in archaeozoological material. However, diagnostic imaging techniques such as radiography should be implemented to confirm or exclude suspected alterations and to help the classification of the specimen by etiology.