Nowadays, hematopoietic stem cell transplantation (HSCT) is a common procedure in hematology units within reference centers, mainly for the treatment of hematological malignancies such as multiple myeloma, lymphoma, and acute leukemia. Nevertheless, HSCT has much wider applications, namely in autoimmune diseases, congenital metabolic defects, and hemoglobinopathies. Thalassemia major and sickle cell disease make up the most frequent hereditary hemoglobinopathies worldwide. Despite advances on the prevention and treatment of complications related to these diseases, the only curative approach available resides in allogeneic HSCT. The main challenges of this treatment remain focused on the toxicity of pre-transplant conditioning regimens and short-term transplant related complications like graft-versus-host disease, infections, and disease recurrence. Thus, it is crucial to establish a balance between the risk vs benefit of HSCT for each patient and follow the available guidelines for both diseases. Recently, gene therapy has become a real alternative to allogeneic HSCT. Recent advances in molecular biology methods have provided more accurate and reliable gene editing techniques such as the CRISP/CAS9 system. The long-term outcome of gene manipulation procedures remains uncertain, especially in