The management of proctitis in patients who have undergone very high-dose conformal radiotherapy is extremely challenging. The fibrosis-necrosis, fistulae, and hemorrhage induced by pelvic over-irradiation have an impact on morbidity. Augmenting tissue repair by the use of mesenchymal stem cells (MSCs) may be an important advance in treating radiation-induced toxicity. Using a pre-clinical pig model, we investigated the effect of autologous bone marrow derived-MSCs on high-dose radiation-induced proctitis. Irradiated pigs received repeated intravenous administrations of autologous bone marrow-derived. Immunostaining and real-time PCR analysis were used to assess the MSCs effect on inflammation, extracellular matrix remodeling and angiogenesis, in radiation-induced anorectal and colon damages. In human, such as in pig rectal overexposition induced mucosal damage (crypts depletion, macrophages infiltration and fibrosis). In pig model repeated administrations of MSCs controlled systemic inflammation, reduced in situ in both expression of inflammatory cytokines, macrophage recruitment and augmented IL-10 expression in rectal mucosa. MSCs injections limited radiation-induced fibrosis by reducing collagen deposition and expression of Col1a2/Col3a1 and TGF-/CTGF, and by modifying the MMP/TIMP balance. In a pig model of proctitis, repeated injections of MSCs effectively reduced inflammation and fibrosis and are a promising therapy for radiation-induced rectal severe damages.