Two key properties of short chain fructooligosaccharides (sc-FOS) which lead to physiological functions are indigestibility in the small intestine and fermentability in the colon. Sc-FOS is converted into short chain fatty acids (SCFAs) by intestinal bacteria in the colon and absorbed. Through the metabolic pathway, sc-FOS improves gastrointestinal (GI) condition such as relief from constipation, formation of preferable intestinal microflora and intestinal immunomodulation those are known as prebiotics' function. Besides improvement of GI condition, dietary sc-FOS influences on calcium and magnesium absorption in the colon. A major mineral absorption site is the small intestine, but the colon also works as a Ca and Mg absorption site with an aid of SCFAs made from sc-FOS. Furthermore dietary sc-FOS influences on bioavailability of soy-isoflavones. Plasma and urinal concentration of Genistein and Daidzein, aglycones of Daidzin and Genistin, are higher in the rat fed with sc-FOS than the control rat. An additive effect of dietary isoflavone and sc-FOS was observed on the bone mineral density in OVX mice and moreover sc-FOS increased ceacal beta-glycosidase activity and equol production. These results suggest that FOS increase the bioavailability of isoflavones.