BackgroundThe role of allogeneic hematopoietic stem cell transplantation (allo‐HSCT) in patients <3 years of age remains controversial. Data on haploidentical donor (HID) transplants in this age group is limited.Patients and MethodsWe retrospectively analyzed the prognosis of 97 patients with acute leukemia aged <3 years who underwent HID transplantation at our institute.ResultsWith a median follow‐up of 45 months, the 3‐year disease‐free survival (DFS), overall survival (OS), and 3‐year cumulative incidence rate of treatment‐related mortality were 69.3% (95% confidence interval (CI): 59.9%–78.7%), 74.2% (95% CI: 65.2%–83.2%), and 3.6% (95% CI: 0.9%–9.7%) in all 97 patients, respectively. The 3‐year DFS and OS rate in patients diagnosed <1 year and patients diagnosed ≥1 year were comparable: 77.8% (95% CI: 62.2%–93.4%) versus 66.3% (95% CI: 55.0%–77.6%, p = .253) and 82.5% (95% CI: 66.3–98.7%) versus 72.8% (95% CI: 61.9%–83.7%, p = .153), respectively. At the last follow‐up, 23 patients had died, and 20 had died of relapse. Multivariate analysis revealed that positive pre‐HSCT flow cytometric minimal residual disease (hazard ratio 5.605, p = .000) and AML‐M7 expression (hazard ratio 2.906, p = .014) were independent adverse prognostic variables for relapse.ConclusionsHID transplantation is potent and safe for infants and young patients with acute leukemia. Relapse is the primary cause of treatment failure.