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Several factors may interfere with the response to hematopoietic stem cell transplantation (HSCT) in myelodysplastic syndrome (MDS). To evaluate the effect of cell source and type of conditioning on HSCT outcome in MDS. We analyzed data from 258 MDS patients from the Latin American transplant registry in Brazil and Uruguay from 1988 to 2019. The statistics were performed on SPSS v.23.1, considering significant p < 0.05. A predominance of males (56.2%) and Caucasian individuals (84.5%) was observed. The most frequent age group was 51 to 60 years (2 -79 years) (26%). When stratified according to the Prognosis Scoring System (IPSS-R), 0.78% were classified as very low risk, 11.2% as low risk, 24% as intermediate risk, 21.3% as high risk and 4.7% as very high risk. A total of 38% of patients could not be classified according to the IPSS-R due to lack of data, such as cytogenetics. In myeloablative conditioning (MAC) (78.7%) the regimens were (bulssulfan/fludarabine, bulssulfan/cyclophosphamide, with or without total body irradiation (ICT)). Reduced intensity (RIC) (15.9%) was (bulssulfan/fludarabine, bulssulfan/cyclosphosphamide at reduced doses, with or without ICT and FluMel). The cell source was bone marrow (BM) (52.7%), peripheral blood (PB) (45.3%) and cord blood (2%). Major post-HSCT complications included acute (37.2%) and chronic (28.7%) graft versus host disease (GVHD). Regarding the possible predictors of acute, chronic GvHD and death, there was an association between type of cell source and the death outcome (p = 0.0336). Moreover, there was a significant association between acute GvHD and conditioning regimen (p = 0.0127) and cell source (p = 0.0004). There was also an association of chronic GvHD with the conditioning regimen (p <0.0001) and donor type (p = 0.0246). In binary logistic regression analysis, MAC was 2.81 times more likely to develop acute GVHD than RIC (OR: 2.81; 95%CI:1.1-7.15; p = 0.031). MAC was also 7.35 times more likely to develop chronic GVHD than RIC (OR: 0.14; 95%CI:0.03-0.6; p = 0.008). The type of donor showed no influence on the outcome acute, chronic GVHD and death after HSCT. Cell source type was a significant predictor of death in patients. BM was 2.09 times more likely to death than PB (OR:2.09; 95%CI:1.25-3.51; p = 0.005) Overall survival was higher with PB (p = 0.0478). The overall survival at 6 years was 51.33%. The results demonstrate the impact of conditioning and cell source on the HSCT outcome and reinforce the need for an appropriate assessment for better conduction results optimization. [ABSTRACT FROM AUTHOR]