The question of whether iron deficiency has direct adverse effects on vertebral trabecular bone and long bones was answered by this study. Four groups of female weanling rats were fed for 5 wk diets that were 1) control; 2) calcium restricted, 1.0 g Ca/kg diet; 3) iron deficient, <8 mg Fe/kg diet; or 4) control, pair-fed to the iron-deficient group. Whole body and femur DEXA analysis revealed that calcium-restricted and iron-deficient rats had lower bone mineral density (BMD) and content (BMC) than pair-fed and control rats. However, pair-fed rats also had decreased BMD and BMC compared to control rats. The third lumbar trabecular bone microarchitecture in both diet-restricted groups had decreased bone volume fraction (BV/TV) and trabecular number and thickness, a less favorable structural model index, and increased trabecular separation compared with the controls and the pair-fed groups as determined by microcomputer tomography. The control and pair-fed groups did not differ from one another, suggesting that iron deficiency and calcium restriction affected vertebrae independently of food intake and body weight. Finite element analysis revealed lower force to compress the vertebrae and lower stiffness but greater von Mises stress in calcium-restricted and iron-deficient groups compared to the control and pair-fed groups. Urinary deoxypyridinium crosslinks, serum osteocalcin, and cholcalciferol were increased in calcium-restricted rats compared to the other 3 groups. Using micro-CT imaging technology, this study demonstrated microarchitectural pathology due to iron deficiency upon vertebral trabecular bone compared to the control and pair-fed rats, although not to the same extent as severe calcium restriction.