Background: Prolyl hydroxylases (PHDs) are linked to inflammatory bowel diseases (IBD); however, the exact role of PHD3, a member of PHD family, in IBD is unknown. Results: Deletion of Phd3 in mice intestinal epithelial cells causes spontaneous colitis. Conclusion: PHD3 protects the intestinal epithelial barrier function. Significance: The results are helpful for the development of therapeutic strategies for IBD.