Myelodysplastic Syndrome (MDS) is a clonal disorder characterized by dysplastic changes and ineffective hematopoiesis. The ineffective hematopoiesis is considered as the results of excessive apoptosis of bone marrow (BM) hematopoietic cells. Recently, immunosuppressive therapy is effective in some hypoplastic MDS patients, resulting in the dramatic improvement of complete blood counts. To elucidate the difference between MDS patients with hypoplasia and normo/hyperplasia in BM, we measured the frequency of apoptosis in each lineage CD34+ BM cells in 35 MDS (12 RA patients with hypoplastic BM, 9 RA, 7 RAEB, and 7 RAEB-t patients with normo/hyperplastic BM) at diagnosis by three color flow cytometric analysis. Apototic cells were analyzed by PE labeled AnnexinV. The lineage cell population was identified as CD34+/GlycophorineA+, CD34+/CD33+, CD34+/CD41+, CD34−/GlycophorineA+, CD34−/CD33+ and CD34−/CD41+. In this study, the higher frequency of apoptosis was observed in each lineage CD34+ cells in all MDS patients (n=35, median: 32.2% (range: 6.3–80.5%) in erythroid, 38.0% (8.8–93.3%) in myeloid, 41.4% (10.2–78.4%) in megakaryocytic lineage, p<0.05, respectively), compared to that in normal controls (n=10, 8.5% (1.5–9.9%) in erythroid, 8.5% (2.2–8.8%) in myeloid, 7.7% (4.4–9.3%) in megakaryocytic lineage, respectively). While much higher frequency of apoptosis was observed in each lineage CD34+ cells in hypoplastic MDS patients (n=12, 49.1% (31.2–80.5%) in erythroid, 66.0% (37.8–93.3%) in myeloid, 68.5% (43.4–78.4%) in megakaryocytic lineage, p<0.05, respectively), compared to that in normo/hyperplastic MDS patients (n=23, 28.7% (6.3–69.4%) in erythroid, 30.0% (8.8–61.7%) in myeloid, 29.8% (10.2–58.1%) in megakaryocytic lineage, respectively). The increased frequency of apoptosis in each lineage CD34+ cells decreased after immunosuppressive therapy (n=5, 25.3% (19.8–36.4%) in erythroid, 35.2% (20.1–42.0%) in myeloid, 38.5% (30.6–47.9%) in megakaryocytic lineage, respectively). Our findings suggested that the excessive apoptosis occurred mainly in CD34+ cells in hypoplastic MDS as well as in non-hypoplastic MDS. Much more increased frequency of excessive apoptosis in CD34+ cells resulted in BM hypoplasia in hypoplastic MDS patients. This method is useful to evaluate quantitatively the ineffective hematopoiesis in BM hematopoietic cells.