Simple SummarySingle-cell DNA sequencing is a laboratory technique that analyzes the genetic content of individual cells. In the context of genetically diverse hematological cancers such as acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS), the traditional approach of analyzing genetic material, which typically involves bulk samples of leukemia cells, may miss important mutations that may not be present in all cells. The single-cell DNA technique can better identify genetic mutations associated with disease recurrence and death even after stem-cell transplantation. The paper discusses the background, pitfalls, and applications of this technology when used during transplantation procedures. The use of this technology could potentially translate to better outcomes in AML/MDS patients receiving stem-cell transplantation.AbstractAcute myeloid leukemia (AML) and myelodysplastic syndrome (MDS) are genetically complex and diverse diseases. Such complexity makes challenging the monitoring of response to treatment. Measurable residual disease (MRD) assessment is a powerful tool for monitoring response and guiding therapeutic interventions. This is accomplished through targeted next-generation sequencing (NGS), as well as polymerase chain reaction and multiparameter flow cytometry, to detect genomic aberrations at a previously challenging leukemic cell concentration. A major shortcoming of NGS techniques is the inability to discriminate nonleukemic clonal hematopoiesis. In addition, risk assessment and prognostication become more complicated after hematopoietic stem-cell transplantation (HSCT) due to genotypic drift. To address this, newer sequencing techniques have been developed, leading to more prospective and randomized clinical trials aiming to demonstrate the prognostic utility of single-cell next-generation sequencing in predicting patient outcomes following HSCT. This review discusses the use of single-cell DNA genomics in MRD assessment for AML/MDS, with an emphasis on the HSCT time period, including the challenges with current technologies. We also touch on the potential benefits of single-cell RNA sequencing and analysis of accessible chromatin, which generate high-dimensional data at the cellular resolution for investigational purposes, but not currently used in the clinical setting.