Patients with Fanconi anemia (FA) have a high risk of developing acute myeloid leukemia (AML). In this study, we attempted to identify cell-surface markers for leukemia-initiating cells in FA-AML patients. We found that the IL-3 receptor-α (IL-3Rα) is a promising candidate as an leukemia-initiating cell-specific antigen for FA-AML. Whereas IL-3Rα expression is undetectable on normal CD34⁺CD38⁻ HSCs, it is overexpressed on CD34⁺CD38⁻ cells from FA patients with AML. We examined the leukemia-initiating cell activity of IL-3Rα–positive FA-AML cells in a “humanized” FA xenotransplant model in which we separated AML cells into IL-3Rα–positive and IL-3Rα–negative CD34 fractions and transplanted them into irradiated recipient mice. In all 3 FA-AML samples, only IL-3Rα–positive cells showed significant levels of engraftment and developed leukemia in the recipient mice. The FA CD34⁺IL-3Rα⁺ blasts isolated from leukemic mice exhibited hypersensitivity to IL-3 deprivation and JAK2-STAT5 overactivation after IL-3 treatment. Finally, treatment of FA CD34⁺IL-3Rα⁺ blasts with an IL-3Rα–neutralizing antibody inhibited IL-3–mediated proliferation and STAT5 activation. These results demonstrate that IL-3Rα is a cell-surface marker present on FA-AML leukemia-initiating cells and may be a valuable therapeutic target.