Paroxysmal nocturnal haemoglobinuria (PNH) is an acquired clonal disorder of the haemopoietic stem cell (HSC). The pathogenetic link with bone marrow failure is well recognized; however, the process of clonal expansion of the glycosylphosphatidylinositol (GPI)-deficient cells over normal haemopoiesis remains unclear. We have carried out detailed analysis of the stem cell population in 10 patients with de novo haemolytic PNH using the long-term culture-initiating cells (LTC-IC) assay in parallel with measurements of CD34+ cells and mature haemopoietic progenitors, granulocyte-macrophage colony-forming unit (CFU-GM) and CFU-erythroid [burst-forming units erythroid (BFU-E) + CFU granulocyte/erythroid/macrophage/megakaryocyte (GEMM)]. All patients had hypercellular bone marrows with erythroid hyperplasia, normal blood counts or mild peripheral blood cytopenias, increased reticulocyte counts and evidence of deficient GPI-anchored proteins. We found a significant reduction in the LTC-IC frequency in the CD34+ compartment of PNH patients (mean 2, range 1.3-3.0; n=6) compared with normal donors (mean 13, range 5.2-45.5; n=21) (P<0.0001). Furthermore, there was a significant reduction in the erythroid compartment [CFU-E/105 bone marrow mononuclear cells (BMMC) and CFU-E/105 CD34+ cells] of PNH patients, but no significant difference in the granulocyte-monocyte precursors (CFU-GM/105 BMMC or CFU-GM/105 CD34+ cells) compared with normal donors, suggesting that there is a defect in the early stem cell pool in PNH patients without clinical or haematological evidence of bone marrow failure.