In MDS, the bone marrow produces abnormal, immature blood cells called blast cells. Imprecise, in half of pediatric MDS, blast count is normal. A retrospective observational study was conducted to review the outcome of our HCT in pediatric patients with MDS. Record of 35 MDS patients after BMT, 1993-2016, were reviewed. Median age at transplant was 4 yrs (0.8-14.8) and median time to transplant from diagnosis 8.1 (2.3-102.5) months. TRM was 17.1% (6); [low risk (LR) = 5 (19.2%) and high risk (HR) = 1 (11.1%)] MDS group succumbed within first 100 days. The rest were fully engrafted; [low risk = 21 (72.4%) and high risk = 8 (27.6%)]. Primary and secondary graft failure was observed in one patient each (2.9%). VOD was seen in 2 patients (5.7%) and 5 (14.3%) had hemorrhagic cystitis. With a median follow-up of 112.4 months and 12 events of mortality, 3-years OS was 68.1% ± 8.0%. No significant risk factor including age, time to transplant, disease risk group, gender, conditioning regimen, source of stem cells, or a GvHD through uni- or multi-variable analyses were found to be associated with OS. Bu/Cy/±ATG conditioning regimen showed a trend of superiority for OS and EFS in our small series. The relapse incidence in our cohort was 11.5% in LR MDS.