Myelodysplastic syndrome (MDS) is a heterogeneous group of malignant disorders of blood cell production occurring predominantly in elderly patients. While low intensity treatments are appropriate initially in most patients with favorable prognoses, hematopoietic cell transplantation (HCT) is the only curative therapy and is the best therapy for many higher risk patients. In patients who present with lower-risk disease, HCT may be considered at the time of meaningful disease progression. In patients receiving hypomethylating treatment, outcome of HCT is best when performed during response, and HCT is less effective when performed after resistance occurs. Advances over the last 2 decades have markedly improved safety and survival with HCT, and appropriate donors are now available for virtually every patient in whom HCT is indicated. The application of HCT in MDS has expanded significantly over the last few years and its use in MDS promises to continue to grow as results further improve.