This retrospective multicenter study aimed to compare outcomes and evaluate risks associated with allogeneic hematopoietic cell transplantation (allo-HCT) in myelodysplastic syndrome patients aged ≥ 65 versus < 65 years in Latin America, across 38 transplant centers (1988-2023). Of the 441 patients, 70 (16%) were ≥ 65 years (median age 68 ± 3.7). At 5 years, overall survival (OS) was 49.3% in patients ≥ 65 vs. 56.7% in those < 65 (p = 0.49), and progression-free survival (PFS) was 48.4% vs. 56.2% (p = 0.40). The cumulative incidence of relapse was 13.6%, and non-relapse mortality (NRM) 33.8%. After propensity score matching, no significant differences were observed between the age groups in OS (HR = 1.16; 95% CI: 0.76-1.77; p = 0.488), NRM (HR = 1.03; 95% CI: 0.64-1.67; p = 0.90) or PFS (HR = 1.20; 95% CI: 0.779-1.83; p = 0.40). PFS in patients ≥ 65 years was associated with high-risk IPSS-R stratification (p = 0.0056). The age group ≥ 65 years conferred higher risk of relapse compared to patients aged < 65 years (HR = 2.77; 95% CI: 1.07-7.15; p = 0.035). In patients ≥ 65 years, prevalence risk was associated to male sex, reduced-intensity conditioning, mobilized blood cells, and prior treatment, while in those < 65 years, to complications and chronic GVHD (p < 0.05). HCT is feasible in elderly patients. However, age may influence disease progression in very high-risk elderly patients and risk of relapse after transplantation.