Human skeletal remains from prehistoric Chile's semi-arid north were analyzed using the Western Hemisphere Health Index to ascertain if subsistence change from gathering/hunting to agriculture was accompanied by a decline in physiological stress as measured by common skeletal stress markers for these coastal populations. Individuals analyzed dated to the Archaic (c. 7000 BC-200 AD, n=95) and Diaguita (c. 1000-1536 AD, n=75) periods. The Archaic individuals practiced gathering and hunting subsistence, relying on desert and ocean resources. The Diaguita practiced a subsistence strategy including agriculture, food collecting from the Pacific, and camelid pastoralism. As per health index methodology, seven indicators were scored (stature, linear enamel hypoplasia, dental disease, cribra orbitalia/porotic hyperostosis, infection, degenerative joint disease, and trauma). Results indicated equal health index values for both samples, although there were some differences in individual indicator values. The risk of having any pathology did not increase with age-at-death. Essentially, health as measured by common stress markers did not vary substantially after subsistence change. Such results are further evidence that the hypothesis of a health decline after subsistence change to agriculture is not always demonstrated, and it is important to elucidate what buffering variables beyond diet, to include cultural adaptations, may be at play.