The selection of a treatment strategy before allogeneic hematopoietic stem cell transplant (HSCT) for myelodysplastic syndrome is a delicate process. The expected relapse risk and nonrelapse mortality after HSCT and the response rates to the pretransplant strategies all play a role in this process. Fit patients younger than 60 to 65 years with > 10% marrow blasts and without high-risk cytogenetic abnormalities should be seriously considered for intensive chemotherapy (ICT) to reduce tumor load before HSCT. Other patients up to the age of 75 years may be considered for hypomethylating agent therapy before transplant. Patients with high-risk cytogenetic abnormalities should be treated in investigational protocols if they are not candidates for ICT.