Vitamin D receptor (VDR) regulates the biological actions of the active vitamin D metabolite, 1α,25-dihydroxyvitamin D3. Evidence strongly supports that VDR signaling is involved in the genetic, environmental, immune, and microbial aspects of inflammatory bowel diseases (IBD). Low VDR expression and dysfunction of vitamin D/VDR signaling are reported in patients with both Crohn’s disease and ulcerative colitis. Knockout of ATG16L1, a VDR target gene and an IBD risk gene, in myeloid cells promotes dysbiosis.