We examined whether the enhanced mineral absorption resulting from fructooligosaccharide (FOS) consumption affects femoral bone structure and mineral concentrations, using histomorphometrical and X-ray microanalysis. Male Wistar rats (n = 16; 42 d old) were divided into two groups, a control group (n = 8) and a FOS group (5 g/100 g FOS in the diet, n = 8). After a 3-d adaptation period, constant amounts of calcium (95 mg/d) and magnesium (8 mg/d) were fed to the rats in each group, using a pair-feeding protocol. At age 60 d, a 3-d metabolic study was initiated. Calcium and magnesium absorptions were calculated. The rats were then killed, and the right femur was embedded in polyester resin. The distal metaphysis was sagittal-sectioned, and the middle of the diaphysis and neck were cross-sectioned. Calcium, magnesium and phosphorus concentrations in the three samples were then measured. Calcium and magnesium absorptions were significantly greater in FOS-fed rats. Trabecular bone volume at the metaphysis and bone volume at the neck of the femur in FOS-fed rats were also significantly greater than those in control rats. The mineral concentration (Ca, Mg and P) in each region of the bone surface was greater in FOS-fed rats. There was a significant relationship between absorbed calcium and calcium concentrations in bone (r = 0.722, P < 0.001), and a similar relationship was found for magnesium (r = 0.720, P < 0.001). These results suggest that the enhanced calcium and magnesium absorption due to FOS consumption might enhance femoral bone volume and mineral concentrations.