Complex fermentable carbohydrates, such as inulin-type fructans have been shown to improve Mg2+ absorption in the hindgut and body stores. The mechanisms for this are not well understood. The newly identified transient receptor potential melastatin 6 and 7 (TRPM6 and TRPM7) channels have been shown to function in active epithelial Mg2+ transport in the apical membrane of epithelial cells, the kidney and intestine and to be regulated by dietary intake. To determine the modulation of TRPM6 and TRPM7 expression in kidney and large intestine by long-chain inulin ingestion, C57B16J mice were fed a control or a long-chain inulin enriched diet (65 g of inulin/kg diet) for two weeks. Our results show that the inulin-enriched diet ameliorated Mg2+ absorption and Mg2+ bone stores. These features were accompanied by increased TRPM6 and TRPM7 expression in the hindgut. Downregulation of TRPM6 in the kidney of inulin fed mice could be related to reduced Mg2+ reabsorption and supports the beneficial effect of dietary fibers on Mg2+ absorption and stores. Inulin ingestion also modulates TRPM6 and TRPM7 expression in the large intestine. The origin and role of this modulation is not known. Changes in Mg2+ fluxes, lower pH of the digestive content and increased cell proliferation may be involved.