In 1991, a 27-year-old woman who presented with recurrent oral and genital ulcers, fever, and erythema nodosum was diagnosed with Behçet's disease (BD). Her symptoms were refractory to conventional therapy. In 1999, pancytopenia was noticed in this patient for the first time, and in 2000, her white blood cell count decreased to 0.94×109/l with 1% myeloblasts and 24% neutrophils. Bone marrow examination showed mild hypocellularity with 8% myeloblasts and 6% mature neutrophils with dysplastic features. A diagnosis of myelodysplastic syndrome (MDS)-refractory anemia with excess blasts was made. Despite marked neutropenia, the BD symptoms continued. Since her neutropenia worsened to 0.24×109/l with 21% neutrophils, the patient underwent cord blood transplantation (CBT) from an unrelated donor in July 2001. Myeloid engraftment was documented on day 26. Grade I acute graft-versus-host disease occurred, but resolved spontaneously. Cyclosporin treatment was reduced gradually and discontinued 6 months after CBT. Twenty-three months after CBT, the patient is doing well and has no signs or symptoms of BD or MDS. These observations suggest that allogeneic hematopoietic stem cell transplantation, which encompasses CBT, may be an effective therapy in patients with high-risk aggressive BD.