Non-steroidal anti-inflammatory drug (NSAID)-induced epithelial cell damage occurs not only in the stomach but also in the intestines and colon. Although several studies have investigated the related mechanism underlying lower gastrointestinal tract injury, the details of this mechanism are still unclear. Since it was reported that protein degradation might play an important role, herein, we focused on one of the major ubiquitin E3 ligases, the von Hippel-Lindau protein (pVHL). To understand whether pVHL is involved in the observed cell damage, we examined whether indomethacin (IM) treatment affects pVHL expression in the rat IEC6 intestinal epithelial cell line. We showed that pVHL was upregulated after IM treatment through increased oxidative stress. pVHL siRNA prevented cell injury after IM treatment. Furthermore, the collagen I and HIF-1α protein band intensities were both decreased after IM treatment, whereas MG132 reversed the proteins' downregulation, indicating that the IM treatment-induced downregulation was due to the degradation through pVHL-mediated polyubiquitination. Co-immunoprecipitation showed that pVHL interacted with both collagen I and HIF-1α. The degradation of collagen I and HIF-1α after IM treatment was reversed by siVHL or a Mn-SOD mimetic, Mn(III)TMPyP. The expression of collagen I and HIF-1α was correlated with pVHL expression level, whereas only HIF-1α, not collagen I, was upregulated after the treatment of a prolyl hydroxylase inhibitor, CoCl2. The effect of pVHL on the intestinal epithelium after IM treatment was also tested in vivo. Western blot analyses were used to test whether pVHL's protein expression level might increase after oral administration of IM to mice, and which showed that IM upregulated pVHL expression and degraded collagen I and HIF-1α, consistent with the data obtained in IEC6 cells. These data suggested that intestinal epithelial cells were injured after IM treatment through the pVHL overexpression-induced degradation of collagen I or HIF-1α. Therefore, pVHL might be a molecular target for IM-induced intestinal epithelial cell injury.