The landscape of transplantation in myelodysplastic syndrome (MDS) has evolved rapidly in the last decade, driven mostly by advances in patient selection through better risk stratification, increasing age of allogeneic recipients, introduction of reduced-intensity conditioning regimens, increased availability of unrelated donors, new donor sources, and improvements in transplant technology and supportive care. Despite these advances, several issues, mostly centering on approaches to improve post-transplant survival while minimizing transplant-related mortality, continue to present significant challenges. Advances in understanding the molecular pathogenesis of MDS have made it feasible to construct clinically useful risk models that integrate prognostic genes with conventional risk parameters for better selection of patients likely to benefit from hematopoietic cell transplantation. Simultaneous research efforts in several areas, including comorbidity assessment, novel preparative regimens, optimal pretransplant cytoreductive strategy, and post-transplantation therapies, are expected to improve long-term disease-free survival and quality of life.