Recently, encouraging data provided long-awaited hope for gene therapy as a cure for sickle cell disease (SCD). Nevertheless, the suspension of the bluebird bio gene therapy trial (ClinicalTrials.gov: NCT02140554) after participants developed acute myeloid leukemia/myelodysplastic syndrome (AML/MDS) is concerning. Potential possibilities for these cases include busulfan, insertional mutagenesis, both or neither. Busulfan was considered the cause in the first reported case, as the transgene was not present in the AML/MDS. However, busulfan is unlikely to have contributed to the most recent case. The transgene was present in the patient's malignant cells, indicating they were infused after busulfan treatment. Several lines of evidence suggest an alternative explanation for events in the bluebird bio trial, including that SCD population studies show an increased relative, but a low absolute, risk of AML/MDS. We propose a new hypothesis: after gene therapy for SCD, the stress of switching from homeostatic to regenerative hematopoiesis by transplanted cells drives clonal expansion and leukemogenic transformation of pre-existing premalignant clones, eventually resulting in AML/MDS. Evidence validating our hypothesis will support pre-screening individuals with SCD for pre-leukemic progenitors before gene therapy. Until a viable, safe strategy has been implemented to resume gene therapy in adults with severe SCD, reasonable alternative curative therapy should be considered for children and adults with severe SCD. Currently, open multi-center clinical trials are incorporating nonmyeloablative conditioning, related haploidentical donors, and post-transplantation cyclophosphamide. Preliminary results from these trials appear promising and NIH-sponsored trials are ongoing in pediatric and adult individuals with SCD using this platform.