We carried out a balance study to examine the effects of isomaltulose, lactose, isomalt, and isomaltulose-based oligomers (IBOs) on mineral (calcium, magnesium, phosphorus, and iron) absorption and retention. Four-week-old male Wistar rats were divided into five groups of six rats each and fed a basal diet or diet the containing either 5% isomaltulose, 5% lactose, 5% isomalts or isomaltulose-based oligomers (IBOs) ad libitum for 16 d. After 1 wk, the animals were subjected to a 5-d mineral (calcium, magnesium, phosphorus, and iron) balance study. The isomalt feeding, as well as the IBOs feeding, led to significantly elevated mineral absorption and retention. On the other hand, lactose feeding, widely known to enhance calcium absorption, increased only calcium absorption and isomaltulose feeding did not affect mineral absorption or retention. The organic acids in cecum contents were increased by IBOs or isomalt feeding. Succinic and acetic acids in cecum contents were significantly increased by IBOs feeding. Similarly, succinic, acetic, and i-valeric acids and total amount of organic acid in cecum content were significantly increased by isomalt feeding. Although the organic acids in cecum contents were increased by IBOs or isomalt feeding, the pH values and acidity in cecum contents were not changed by IBOs or isomalt feeding. The effect of addition of various organic acids to the mucosal fluid was examined with in vitro study using a hindgut segment. By the addition of acetic acid, and butyric acid, the mineral (calcium, magnesium, and phosphorus) uptake was increased.