To date, the only treatment option with curative potential for patients suffering from myelodysplastic syndromes (MDS) is allogeneic stem cell transplantation (allo-SCT). However, patient selection for this procedure as well as the choice of the appropriate pre-transplant regime remain challenging. This review discusses both intensive chemotherapy and hypomethylating agents (HMAs) as debulking strategies. Current evidence on the use of AML-like intense chemotherapy suggests that this represents a valuable option especially in fitter and younger MDS patients with aggressive disease, whereas HMAs seem especially indicated in patients presenting with certain mutations and less proliferative disease in order to bridge them to transplant. The actual need for pre-transplant cytoreduction strongly depends on donor availability and disease progression: upfront allo-SCT might be considered for patients with slowly progressing MDS if a donor is readily available. Common to the data discussed in this review is their retrospective nature, making clear recommendations in terms of debulking strategy difficult. Prospective randomized trials are required to explicitly answer this question in the future.