Behçet's disease is a chronic, relapsing, inflammatory disease of unknown origin. The association of myelodysplastic syndrome and Behçet's disease is rare, and recent reports have indicated that immunosuppressive agents alone are not sufficient to control Behçet's disease associated with MDS and many patients die of infection or hemorrhage. We report a case of MDS with intestinal Behçet's disease. We performed cord blood transplantation with a myeloablative regimen as the primary treatment. The patient achieved complete remission for both diseases, which continued for more than 16 months. Our experience suggests that CBT may provide a potent therapeutic option for the treatment of MDS-related Behçet's disease.