Simple Summary The authors first present eight animal remains showing pathological changes, found in two Middle Neolithic assemblages in northern and western Hungary. Among the disorders identified in this set of animal remains, linear enamel hypoplasia was recognized for the first time in the Hungarian Neolithic. These Middle Neolithic finds were then reviewed within the context of palaeopathological data from the better-represented Early and Late Neolithic and, subsequent, (Late Copper Age and Early Bronze Age) prehistoric periods. Along with the increasing number of cases observed, patterns have begun to emerge in the taxonomic distribution of pathological lesions. The apparent great variability of the materials is, thus, discussed in terms of assemblage size, inter-observer bias and, ultimately, changes in prehistoric animal-keeping practices. Eight newly identified pathological animal remains identified in two Middle Neolithic assemblages (ca 5330-4940 calBC) in northern and western Hungary were placed within the broader context of relevant prehistoric finds. The aim was to understand the underrepresented Middle Neolithic finds in light of the better-known cases from other prehistoric periods. The newly reported cases include arthritic and inflammatory lesions, as well as dental disorders, such as linear enamel hypoplasia, recognized for the first time in the Hungarian Neolithic. Identifications were based on bone macromorphology. When large samples are available, the frequencies of pathological bone specimens reflect the taxonomic composition. Along with the increasing number of cases, longevity related to exploitation for secondary products also became manifest. Therefore, the effects of assemblage size, disease classification and differences between authors (related to training and the time of publication) need to be considered before pathological lesions can be interpreted in terms of diachronic changes in animal husbandry.