AbstractThis retrospective study examined the clinical significance of FCM‐MRD in 36 patients with ALL and 29 patients with AML after their first allogeneic HSCT. Hematological (FCM‐MRD ≥5.0%) and molecular relapse (FCM‐MRD <5.0%) were first detected in 10 and two patients with ALL and in seven and eight patients with AML, respectively. Eight of 10 patients with molecular relapse eventually progressed to hematological relapse, although most were treated with immunological intervention by aggressive discontinuation of immunosuppressive therapy or donor lymphocyte infusion. Among these 12 patients, four of seven patients that obtained MRD^neg CR following post‐transplant chemotherapy remain alive and disease‐free after their second HSCT; however, all five patients who underwent a second HSCT in non‐CR died of disease or treatment‐related complications. As the FCM‐MRD monitoring system used in the current study was probably not sensitive enough to detect MRD, which could be elucidated by immunological intervention, more sensitive diagnostic tools are mandatory for post‐transplant MRD monitoring. Additional studies are required to address the impact of presecond transplant MRD on the clinical outcome of second HSCT.