The Fuegians, extinct inhabitants of Tierra del Fuego, were an exemplary case of a cold-adapted population capable of living in extreme weather conditions without any adequate clothing, however the mechanisms of their extraordinary resistance to cold remain enigmatic. Brown adipose tissue (BAT) plays a crucial role in this kind of adaptation besides having a protective role on the detrimental effect of low temperatures on bone structure. Skeletal remains of 12 adult Fuegians were analyzed for bone mineral density and structure. We show that, despite the unfavorable climate, bone mineral density of Fuegians was close to that seen in BAT-expressing modern humans of temperate zones. Furthermore, we report significant differences between Fuegians and other cold-adapted populations in the frequency of the Homeobox protein Hox-C4 (HOXC4) rs190771160 variant, a gene involved in BAT differentiation, whose identified variant is predicted to upregulate HOXC4 expression. Greater BAT accumulation might therefore explain the Fuegians extreme cold-resistance and the protection of their skeletons against major cold-related damage. Our results increase our understanding of how ecological challenges have been important drivers of genetic and environmental factors interactions.