Palaeopathology, the study of diseases in past populations, can offer clues as to the state of health of prehistoric humans. Through bone lesions, inequalities in access to resources, issues of violence, and the general evolution of health over time can be studied. In this research, the Final Neolithic and Bell Beaker populations of the site of Petit-Chasseur, in western Switzerland, were studied using a holistic methodology tailored to commingled remains. Results show the two populations did not differ much from one another, and that their health profiles correspond to that of a primary agrarian prehistoric population. Nonetheless, the presence of infectious lesions and trepanations, as well as the particular context of the burial site of Petit- Chasseur, raise further questions. These are addressed in the discussion and conclusion, in which future research perspectives which could lead to answers on who exactly was buried in these megalithic tombs are proposed.