The present study describes a retrospective analysis on the transplant outcome of 56 consecutive myelodysplastic syndrome (MDS) patients according to their response to hypomethylating agents (HMA). While 2-year disease-free survival (DFS) of patients who transformed to acute myeloid leukemia (n = 12) was 25%, that of the remaining MDS patients according to response to HMA was 73.1%, 68.1%, 50.0%, and 20.8% in G-COR (group of continuous response, n = 19), G-NoC (group of no change, n = 15), G-LOR (group of loss of response, n = 6), and G-DP (group of disease progression, n = 4), respectively. When dichotomized as G-COR/G-NoC versus G-LOR/G-DP, significantly different 2-year DFS (71.0% vs. 33.3%; P = 0.004) and relapse (14.1% vs. 46.7%; P = 0.016) were demonstrated. On multivariate analysis, G-LOR/G-DP (hazard ratio [HR], 3.91; P = 0.008) and poor karyotype at transplantation (HR, 2.69; P = 0.017) were the significant predictors for poor DFS, as G-LOR/G-DP was for relapse (HR, 6.28; P = 0.011). DFS was significantly poor in patients with any of the two predictors in all MDS (81.5% vs. 34.9%; P = 0.001) or higher risk MDS (HrMDS) at the time of HMA (80.7% vs. 29.2%; P = 0.005). G-COR showed a trend of better DFS compared to G-NoC among HrMDS (74.6% vs. 36.5%; P = 0.090). These results implicate the significance of response to HMA on HSCT outcomes and support the need for future study to verify the suggested strategy of proceeding to transplantation before LOR or DP, especially for HrMDS.