Aplastic anemia is associated with quantitative and functional abnormalities in the hematopoietic stem cell compartment. Currently, one of the most primitive human hematopoietic progenitor cells that can be functionally assayed in vitro is the long-term culture-initiating cell (LTC-IC). This assay identifies primitive cells that are capable of producing colonies after five weeks of long-term culture using a limiting dilution method. Previous investigators have demonstrated a significant reduction in the frequency of LTC-IC in bone marrow mononuclear cells (BMMC) isolated from aplastic anemia patients when compared to normal donors. However, immunosuppression of hematopoiesis is a prevalent feature of aplastic anemia. Therefore, we assayed the frequency of LTC-IC in cells expressing the CD34 antigen isolated from bone marrow, a population highly enriched for LTC-IC, of both aplastic anemia patients that had received immunosuppressive therapies (IST, n=13) and normal donors (n=28), thereby minimizing continued immunosuppression by T-cells and regulation by other autologous CD34- cells. We describe a significant reduction of LTC-IC frequency in purified CD34+ populations from aplastic patients (P>0.0001), thus demonstrating a functional difference between this phenotypically defined cell population from patients and normal donors.