We examined the effects of isomaltulose-based oligomers (IBOs) on the mineral content of the whole blood, kidney, liver and tibia in calcium deficient and calcium sufficient rats. Twenty-eight Wistar rats were divided equally into 4 groups and fed with the following diets ad libitum for 4 weeks: (1) calcium sufficient diet (Ca+, IBOs-), (2) calcium-sufficient-IBOs supply diet (Ca+, IBOs+), (3) calcium-deficient diet (Ca-, IBOs-), (4) calcium-deficient-IBOs supply diet (Ca-, IBOs+). There were no significant differences in final body weights among the groups. Food consumption in the calcium-deficient groups was higher than that in the calcium-sufficient groups. The tibia weight was significantly decreased, and the calcium, magnesium and phosphorous contents significantly decreased, and iron content was significantly increased in the tibia of calcium-deficient rats. On the other hand, in IBOs feeding rats, tibia weight, and calcium, magnesium and phosphorous contents were significantly increased, and iron content was significantly decreased. These findings suggest that IBOs feeding improves mineral retention especially in a state of calcium deficiency.