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Studies have shown second allogeneic hematopoietic stem cell transplant (HSCT) to have a potential role in treating relapse after HSCT. We sought to evaluate the outcome of second allogeneic HSCT for children with relapsed leukemia with focus on factors that potentially improve outcome. Thirty-eight children were identified. The median time between transplants was 18.6 months (range 6.7-50.1 months). With median follow-up of 44 months the 2-year overall survival (OS) was 59.1 ± 8.2%. The leukemia-free survival was 51.8 ± 8.2% and the non-relapse mortality 30.8 ± 7.9%. Eleven patients (30%) died of non-relapse mortality at a median of 37 days (range 16-260 days) from second HSCT. Twenty-one patients developed acute graft-versus-host disease (aGVHD) after second HSCT. Patients who developed aGVHD had lower risk for mortality compared to patients who did not have aGVHD, with a hazard ratio (HR) of 0.27 (95% confidence interval [CI] 0.095-0.788, p-value 0.0163). Similarly, patients who developed aGVHD following second HSCT had lower risk for relapse (HR = 0.21, 95% CI 0.051-0.857, p-value 0.0297). Patients who developed aGVHD after first HSCT were less likely to benefit from second HSCT compared to patients without aGVHD after first HSCT. Our experience suggests that second HSCT for pediatric relapsed leukemia can result in acceptable survival and aGVHD is associated with improved outcome.