We investigated the effects of experimental Iodine (I) and/or selenium (Se) depletion on bone quality in young rats. I and Se status and growth in animals were assessed. Weight gain was decreased by I depletion in all animals and by Se depletion in males. I and Se depletion independently decreased bone length and mineral area (BMA) in tibia and femur and Se depletion decreased femur cortical thickness. There was higher bone turnover and lipid oxidation, and lower bone ash weight in male rats. BMA and bone mineral density in vertebra, and bone mineral content in tibia, femur and vertebra were reduced by Se depletion in male rats. Proximal tibia and L3 trabecular bone had a better structure in females than males and when Se was adequate, the deficiency of I increased the structural quality of both tibia and L3 trabecular bone.Tibia cortical bone volume and thickness were higher in males when Se was adequate. The compressive strength of L3 trabecular bone and the bending strength of femur were higher in females. The breaking force of femur was higher in I and Se adequate rats, and the adequacy of I increased femur stiffness in females.