Fructooligosaccharides (FOS) are indigestible oligosaccharides that increase calcium absorption by the colorectum in rats, but the underlying mechanisms remain unclear. We therefore investigated the effects of FOS on expressions of genes involved with calcium absorption in rat colorectal mucosa cells. After feeding a diet containing FOS (100 g/kg diet) to rats for 2 d, we investigated gene transcripts of transient receptor potential vanilloid type 6 (TRPV6), calbindin-D9k, and plasma membrane calcium-ATPase 1b (PMCA1b). The FOS diet increased expression of TRPV6 and calbindin-D9k but did not affect PMCA1b expression. Because FOS could not directly affect gene expression, SCFA formed as fermentation products of FOS were considered as likely intermediates. SCFA (2.0 mmol/L) were thus added to Caco-2 human colonic epithelial cells, resulting in significantly increased mRNA expression of TRPV6. To ascertain the effects of SCFA on mRNA expression, a genomic clone of TRPV6 was isolated. Using luciferase reporter assay, a segment between -71 nucleotides and the translation start site was found to contain a positive responsive element to SCFA. These results suggest that FOS increase calcium absorption by increasing mRNA expression of TRPV6 in rat colorectum, and cell culture analysis indicated that SCFA, as fermentation products of FOS, are involved in the increased mRNA expression of TRPV6. We found for the first time, to our knowledge, that regulation of TRPV6 gene expression by SCFA may be a molecular mechanism involved in the promotion of calcium absorption by FOS in rats.