This data article displays a 10-color/12-parameter flow cytometric assay that was used for the acquisition and analyses of the Ki-67 positive fractions (Ki-67 proliferative indices) and Bcl-2 positive fractions (Bcl-2 anti-apoptotic indices) of the different myeloid bone marrow (BM) cell population in non-malignant BM, myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). Here, BCL2 is linked to myelodysplastic syndrome.