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Feeding mineral-deficient diets enhances absorptive efficiency as an attempt of the body to compensate for the lack of an essential nutrient. Under certain circumstances, it does not succeed; and nutritional deficiency is produced. Our hypothesis was that inulin-type fructans (ITF), which are known to affect mineral absorption, could increase Ca and Fe bioavailability in Ca- and Fe-deficient rats. Male Wistar rats (n = 48, 4 weeks old) were assigned to 1 of 8 groups derived from 2 x 2 x 2 factorial design with 2 levels of added Fe (0 and 35 mg/kg), Ca (0 and 5 g/kg), and ITF (0 and 100 g/kg) for 33 days. The Fe status (hemoglobin, serum Fe, total Fe-binding capacity, transferrin saturation, liver minerals) was evaluated. Tibia minerals (Ca, Mg, and Zn), bone strength, and histomorphometry were determined. In nondeficient rats, ITF supplementation did not affect Fe status or organ minerals, with the exception of tibia Mg. Moreover, ITF improved bone resilience and led to a reduction in eroded surface per body surface and number of osteoclasts per area. In Ca-deficient rats, ITF increased liver (Fe and Zn) and tibia (Zn) mineral levels but impaired tibia Mg, yield load, and resilience. In conclusion, ITF worsened the tibia Mg levels and elastic properties when supplemented in Ca-deficient diets. In contrast, although bone Ca was not affected in nondeficient rats under the present experimental conditions, bone quality improved, as demonstrated by a moderate reduction in femur osteoclast resorption and significant increases in tibia Mg content and elasticity.