Stem cell therapy is the administration of stem cells to a patient to treat or prevent a disease. Since stem cells possess the long-term self-renewal capacity and provide daughter cells that differentiate into the specialized cells of each tissue, stem cell therapy will theoretically improve the disease condition for the lifetime of the patient. As the most widely used stem cell therapy, bone marrow transplantation is the treatment of choice for many kinds of blood disorders, including anemias, leukemias, lymphomas, and rare immunodeficiency diseases. For the fatal genetic blood disorder Fanconi anemia, allogeneic bone marrow transplantation has remained the only curative treatment. But the recent advances in stem cell and gene therapy fields may provide promising opportunities for an alternative or even better management of Fanconi anemia. Many of these new ideas and opportunities are also useful for treating other blood diseases that affect hematopoietic stem cells, such as sickle cell anemia, severe combined immunodeficiencies, and beta-thalassemias. In this chapter, these advances along with their challenges and limitations will be thoroughly discussed.