To clarify whether measurement of serum haptoglobin (Hp) has impact on understanding pathophysiology in bone marrow failure (BMF) syndromes, we investigated concentrations of serum Hp by nephelometric procedure in 156 Japanese patients with BMF, including 54 aplastic anemia (AA), 50 paroxysmal nocturnal hemoglobinuria (PNH), and 52 myelodysplastic syndromes (MDS) patients. The frequencies with low concentrations of serum Hp (<42 mg/dL) in PNH patients (98.0%) were significantly higher than those in AA (27.8%; P < 0.0001) and MDS (38.5%; P < 0.0001) patients. In AA patients, white blood cell (WBC), absolute neutrophil, and platelet counts were significantly decreased in the group (n = 15) with low concentrations of serum Hp than in that (n = 39) with normal concentrations of it, and WBC counts were positively correlated with concentrations of serum Hp, suggesting that WBC counts may affect the concentrations. In MDS patients, hemoglobin concentrations and serum iron were significantly decreased and increased, respectively, in the group (n = 20) with low concentrations of serum Hp than in that (n = 32) with normal concentrations of it, and the values of serum iron were inversely correlated with concentrations of serum Hp, suggesting that ineffective erythropoiesis may affect the concentrations. Several AA and MDS patients with low concentrations of serum Hp had Coombs-negative autoimmune hemolytic anemia determined by immunoradiometric assay. In conclusion, several factors in conjunction with pathophysiology contribute to decrease of serum Hp in BMF.