We developed a new type of anal cup for prevention of coprophagy and determined whether the absorption of Ca and Mg and the stimulatory effects of feeding fructo-oligosaccharides (FO) on the absorption of Ca and Mg were altered by prevention of coprophagy in rats. Rats were fed on a FO-free diet or a diet containing 50 g FO/kg for 2 weeks with or without prevention of coprophagy. FO-feeding increased the apparent absorptive ratio of Ca and Mg in rats with or without prevention of coprophagy. However, in the FO-fed groups the absorptive ratio of Mg in rats with prevention of coprophagy was higher than in rats without prevention of coprophagy. The Ca content of the femur was higher in rats fed on the FO-diet than in rats fed on the FO-free diet both with and without coprophagy. In conclusion, FO-feeding increased the absorption of Ca and Mg in rats both with and without coprophagy. Moreover, prevention of coprophagy enhanced the absorption of Mg in rats fed with FO. Coprophagy has to be considered when the effects of luminal fermentation or mineral absorption are examined in rats.