Minimal residual disease (MRD) detected before hematopoietic cell transplantation (HCT) is associated with adverse outcomes in patients with high-risk acute leukemia. However, the ideal time points for post-transplant MRD assessment and the clinical significance of low levels of residual disease in this context are unclear. We conducted a prospective real-world analysis of high-sensitivity flow cytometry MRD performed before and after transplant (at days 30, 60 and 100) in 77 acute leukemia patients. The aim was to evaluate the kinetics of disease elimination and correlate it with transplant outcomes. Pre-transplant MRD was negative in 42 (MRD-) and positive in 35 patients (MRD+). Post-transplant MRD assessment was feasible at day 30 (n = 30, 38.9%), day 60 (n = 27, 35.0%) and day 100 (n = 60, 77.9%). Relapses occurred in 8 patients in the MRD + group (22.9%) and three in the MRD-negative group (7.1%), p = 0.02. Pre-transplant MRD correlated with a decrease in overall survival (OS
87.9% MRD- vs. 54.0% MRD+) and event-free survival (EFS
85.3% MRD- vs. 51.1% MRD+), p = 0.001. Cumulative incidence of relapse (CIR) was 17.5% in MRD + vs. 2.6% in MRD- (p = 0.049). Non-relapse mortality (NRM) was 31.4% in MRD + vs. 12.1% in MRD- (p = 0.019). One-year OS was higher in patients with negative MRD at d100 (92.4%, 95% CI: 0.81-0.971) than positive d100 MRD (53.3%, 95% CI: 0.177-0.796), p <
0.0001. Disease status and d100 MRD were associated with OS, EFS and CIR. Differences in NRM between leukemia types (ALL: 18.9% MRD- vs. 50% MRD+, and AML 0% MRD- vs. 21.7% MRD+, p = 0.0158) were also observed. In conclusion, pre-transplant MRD assessed by highly sensitive flow cytometry accurately identified patients with adverse prognoses. Persistent MRD after HCT could predict relapse with high specificity and clinical sensitivity. These results highlight the importance of incorporating peri-transplant MRD kinetics into the routine treatment of acute leukemia, particularly in low/middle-income countries.