Allogeneic hematopoietic cell transplantation (HCT) is currently the only treatment with curative potential for sickle cell disease (SCD) and beta-thalassemia. HCT was first used to treat SCD and thalassemia more than two decades ago, and with increasing experience this treatment modality has shifted from being an experimental intervention to one in which selected patient populations are targeted for treatment. Recent multicenter clinical studies show an event-free survival (EFS) of 85% after human leukocyte antigen (HLA)-identical sibling transplantation for SCD, using conventional myeloablative conditioning with a backbone of busulfan (BU) and cyclophosphamide (CY) [1-3]. Results of HCT for thalassemia show very similar outcomes, with EFS probabilities that range from 81%-87% [4,5]. However, the risk of graft failure, recurrent disease, graft-versus-host-disease (GVHD), infections, and long-term sequelae of chronic GVHD and endocrinopathies related to Fe overload and myeloablative BU limit broader application of this therapy. Non-myeloablative conditioning regimens may offer a lower risk of toxicity, and investigations to identify a regimen that is sufficiently immunosuppressive to ensure stable engraftment of donor cells are ongoing. Alternative sources of donor hematopoietic cells that include HLA-matched unrelated donor (URD) and umbilical cord blood (UCB), are being pursued for hemoglobinopathies, with promising initial results. This review discusses the successes, challenges and future direction of HCT for SCD and thalassemia.