Both animal hibernation (heterothermy) and human renal osteodystrophy are characterized by high levels of serum parathyroid hormone. To test the hypothesis of hibernation in an extinct human species, we examined the hominin skeletal collection from Sima de los Huesos, Cave Mayor, Atapuerca, Spain, for evidence of hyperparathyroidism. We studied the morphology of the fossilized bones by using macrophotography, microscopy, histology and CT scanning. We found trabecular tunneling and osteitis fibrosa, subperiosteal resorption,‘rotten fence post’ signs,brown tumours, subperiosteal new bone, chondrocalcinosis, rachitic osteoplaques and empty gaps between them, craniotabes, and beading in ribs mostly in the adolescent population of these hominins. Since many of the above lesions are pathognomonic, these extinct hominins suffered annually from renal rickets, secondary hyperparathyroidism, and renal osteodystrophy associated with Chronic Kidney Disease-Mineral and Bone Disorder (CKD-MBD). We suggest these diseases were caused by non-tolerated hibernation in dark cavernous hibernacula. This is evidenced by the rachitic osteoplaques and the gaps between them mainly in the adolescent individuals along with the evidence of healing mainly in the adults. The sublayers in the rachitic osteoplaques point to bouts of arousal from hibernation. The strong projection of the external lip of the femoral trochlea, the rachitic osteoplaques with the empty gaps between them,the “rotten fence post sign”, and the evidence of annual healing caused by non-tolerated hibernation in adolescent individuals, also point to the presence of annually intermittent puberty in this population. The hypothesis of hibernation is consistent with the genetic evidence and the fact that the SH hominins lived during a glacial period. The present work will provide a new insight into the physiological mechanism of early human metabolism which could help in determining the life histories and physiologies of extinct human species.