Since the arrival of Dutch colonists in the Cape of Good Hope, South Africa, Khoesan populations were subjected to severe political and economic marginalisation and often fell prey to racial conflict. 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 remains. The purpose of this study was to assess the health status of the late 19th and early 20th century Khoesan. Skeletal remains housed in two different European institutions were studied. The sample comprised 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 being younger than 20 years of age. 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 this turbulent period and created new awareness regarding a group of severely mistreated individuals. Copyright © 2014 John Wiley & Sons, Ltd.