Background: Patients suffering from Crohn's disease (CD) show increased incidence of low bone mineral density. Investigating this complication is difficult because the exact etiology of CD remains elusive. Mice carrying a deletion in the tumor necrosis factor (TNF) AU-rich elements (ARE) are reported as a model for human CD and are characterized by elevated TNF-alpha levels and inflammations in the terminal ileum. To evaluate whether these mice have a Ca2+ handling problem, this study analyzed the Ca2+ homeostasis in heterozygous TNF Delta ARE mice (TNF Delta ARE/+) in comparison to wildlype littermates. Methods: Beside serum Ca2+ and vitamin D levels, the expression of Ca2+ transporters was analyzed in intestine, kidney and bone using quantitative real-time PCR, Western blot and immunohistochemistry. Bone scans were performed to measure bone parameters. Results: Ca2+ transporters in duodenum (TRPV6, calbindin-D-9K, PMCA1b) and kidney (TRPV5, calbindin-D-28K, NCX1) showed significantly reduced mRNA expression levels in TNF Delta ARE/+ mice, except for renal TRPV5. In bone, only calbindin-D-9K mRNA displayed a significant down-regulation. These findings were supported by declined duodenal calbindin-D-9K and renal calbindin-D-28K protein values. Likely, this down-regulation of Ca2+ transporters in TNF Delta ARE/+ mice is mediated by the 58 +/- 9% reduction in serum 1,25(OH)(2)D-3 levels. Diminished expression of Ca2+ transporters combined with unchanged serum Ca2+ levels assumes Ca2+ loss from bone to compensate for the body's overall Ca2+ shortage. Indeed, microcomputed tomography scanning demonstrated reduced trabecular and corticol bone thickness and volume in TNF Delta ARE/+ mice. This finding is further supported by increased total deoxypyridinoline in serum. Conclusions: Our results imply that TNF Delta ARE/+ mice have a disturbed Ca2+ homeostasis characterized by reduced duodenal and renal Ca2+ transporters, diminished 1,25(OH)(2)D-3 levels, and increased bone resorption associated with profound bone abnormalities.