Decitabine is a hypomethylating agent with activity in myelodysplastic syndrome (MDS). It is largely unknown whether treatment with this drug before allo-SCT will increase the toxicity of the preparative regimen or otherwise affect the results of the transplant. We report the outcome of 17 patients with MDS with a median age of 55.5 years (range, 36–66 years) who underwent an allo-SCT (12 siblings, 5 unrelated) after prior therapy with decitabine. Preparative regimens consisted of fludarabine in combination with BU (n= 8) or melphalan (n= 9). The source of stem cells was marrow in four patients and peripheral blood (PB) in 13 patients. Thirteen patients were in CR within 100 days of transplant. With a median follow-up of 12 months (range, 3–35 months), 11 patients are alive; eight in CR and three with progressive disease. Prior therapy with hypomethylating agents did not increase toxicity and may improve the outcome of allogeneic transplant in MDS and should be evaluated in a prospective trial.