Since the arrival of the Dutch colonists in the Cape, Khoesan populations were subjected to severe political and economical marginalization and often fell prey to racial conflict and genocide. These circumstances persisted until the early 20th century, during which an astonishing number of Khoesan skeletons were transported from South Africa to various locations in Europe, as at the time, different institutions competed to obtain these valuable remains. Due to the above mentioned circumstances, Southern African Khoesan groups suffered from nutritional stress, as well as substandard living conditions. Such living conditions probably did not allow for health care and medical benefits at the time. It will therefore be interesting to evaluate the health status of this group through palaeopathological assessment. Skeletal remains housed in two different European institutions were studied. The sample comprises of 140 specimens from the Rudolf Pöch Skeletal Collection in Vienna, Austria and 15 specimens from the Musée de l’Homme in Paris, France. These individuals represent both sexes and were aged between newborn and 75 years, with 54 individual being younger than 20 years of age and 101 being adults. The aim was to analyse all skeletal lesions. Results indicated high levels of typical disease conditions associated with groups under stress, such as periostitis, cribra orbitalia and porotic hyperostosis. Treponemal disease, rickets, osteoarthritis and trauma were also encountered amongst other more specific indicators of health and disease. This study provided additional knowledge on the health status and lives of the Khoesan people during the turn of the 20th century, as well as focused new awareness on a group of severely mistreated individuals.