 Abstract hematopoietic stem and progenitor cells, HSBCs, are quantified in daily clinical practice by flow cytometry. In this study, we provide proof of concept that HSBCs can also be estimated by targeted DNA methylation, DNM, analysis. The DNM levels at three individual CG dinucleotides, CPG sites, in the genes MY01D, STK17A, and SP140 correlated with CD34-plus cell numbers in mobilized peripheral blood and with blast counts in leukemia. In the future, such epigenetic biomarkers can support the evaluation of stem cell mobilization, HSBC harvesting, or blast count in leukemia. This article was authored by Lidio Bacova, Walter Hubbins, Cordular Engel, and others.