MRD from ctDNA shows comparable sensitivity to bone marrow (BM) MRD in AML and MDS patients after alloSCT. MRD was measured by ddPCR using individual gene mutations as MRD markers. Some patients were MRD positive by ctDNA analysis but MRD negative in mononuclear cells (MNCs) from peripheral blood (PB), indicating a better representation of residual leukemia in ctDNA than PB-MNCs.