Allogeneic hematopoietic stem cell transplantation is still the only potentially curative treatment for patients with myelodysplastic syndromes. Improvements in donor selection, supportive care and the introduction of reduced-intensity conditioning have led to a decrease in early transplant mortality. However, relapse rates have not changed significantly in recent years. Furthermore, treatment options for patients relapsing after hematopoietic stem cell transplantation are limited and often short-lived. Thus, optimizing the post-transplant outcome by maintenance approaches or minimal residual disease-directed preemptive therapy is an important goal of current clinical research. Further strategies aiming at an improved prevention of graft-versus-host disease are currently under investigation.