ObjectiveThe last 1500 endangered Patagonian huemul deer (Hippocamelus bisulcus) exist in > 100 groups which are not recovering. Prevalence of osteopathology in dead huemul was 57+% (Argentina), whereas similar cases in Chile were accompanied by selenium deficiency. The first clinical cases from live wild huemul confirm widespread osteopathology which explains short life spans, low recruitment, and thus absence of population recovery.ResultsThe first-ever radio-collaring of 3 male huemul in Argentina and 3 females, plus a fresh female carcass allowed examination of 7 huemul. Of these, 86% were diseased and clinical pathophysiognomy included lameness, affected hoof, exfoliation of 2–7 incisors, other cranial osteopathologies, and muscle atrophy. The parsimonious explanation for absent population recovery is high prevalence of osteopathology as evidenced earlier in carcasses, and now by these clinical cases. Areas currently used by huemul have reduced selenium bioavailability, very deficient soil levels, and overt selenium deficiency in local livestock and plants. These areas are known to result in primary iodine deficiency which is aggravated by selenium deficiency. The nexus to nutritional ecology of huemul likely is inaccessibility to most fertile lowlands and traditional winter ranges, elimination of migratory traditions, and concomitant elimination of source populations.Electronic supplementary materialThe online version of this article (10.1186/s13104-017-3052-4) contains supplementary material, which is available to authorized users.