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Therapy-related myelodysplastic syndromes (t-MDS) are generally progressive and associated with poorer outcomes than de novo MDS (d-MDS). To evaluate the outcome of allogeneic hematopoietic stem cell transplantation (allo-HSCT) for t-MDS, we conducted a propensity score matched-pair analysis of patients with t-MDS and d-MDS using a nationwide database. A total of 178 patients with t-MDS underwent allo-HSCT between 2001 and 2018, and 178 out of 3123 patients with d-MDS were selected. The probability of 3-year overall survival rate was 40.0% and 50.0% in the t-MDS and d-MDS groups, respectively (p = 0.032). The 3-year transplant-related mortality was 30.9% and 19.0% in the t-MDS and d-MDS groups, respectively (p = 0.005). The 3-year cumulative incidence of relapse was 32.8% and 33.0% in the t-MDS and d-MDS groups, respectively (p = 0.983). A multivariate analysis identified four adverse factors for overall survival in the t-MDS group: age ≥ 55 years (hazard ratio [HR], 2.09; 95% CI, 1.11-3.94; p = 0.023), the poor cytogenetic risk group (HR, 2.19; 95% CI, 1.40-4.19; p = 0.019), performance status at allo-HSCT 2-4 (HR, 2.14; 95% CI, 1.19-3.86; p = 0.011), and a shorter interval from diagnosis to transplantation (8 months; HR, 1.61; 95% CI, 1.00-2.57; p = 0.048). The most frequent cause of transplant-related death was the infectious complications (21.6%) in t-MDS group and organ failure (12.5%) in d-MDS group. In conclusion, allo-HSCT potentially provides long-term remission in patients with t-MDS; however, further efforts to reduce transplant-related death are needed.