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We performed flow cytometric analysis of CD34⁺ cell apoptosis in 59 patients with myelodysplastic syndrome (MDS) or acute myeloid leukaemia (AML) secondary to MDS (MDS‐AML) using annexin V‐FITC, which binds to exposed phosphatidylserine on apoptotic cells. Apoptosis was significantly increased in FAB subtypes RA, RARS and RAEB (<10% blasts) (56.5% (15.1–86.5%)) compared to normal controls (18.5% (3.4–33.4%), P < 0.0001) and RAEB‐t/MDS‐AML (16% (2.1–43.2%), P < 0.0001). There was no correlation between % apoptosis, Full blood count or cytogenetics in any disease category. Two‐colour cytometric analysis of permeabilized CD34⁺ cells stained with antibodies to Bcl‐2, Bcl‐X (anti‐apoptotic), Bax and Bad (pro‐apoptotic), demonstrated significantly higher ratios of pro‐ v anti‐apoptotic proteins in early MDS (2.47 (1.19–9.42) compared to advanced disease (1.14 (0.06–3.32), P = 0 …