Immunoglobulin-E-mediated allergy (type I allergy) is a T-helper-2-mediated disease with increasing prevalence in industrialized countries. Immunotherapy is available as causative treatment, but an effective preventive strategy is still an unmet need. Molecular chimerism is an attractive experimental approach that induces tolerance through transplantation of autologous hematopoietic stem cells that are genetically modified to express the disease-causing antigen(s). Molecular chimerism leads to permanent and robust tolerance in experimental models of autoimmune diseases and organ transplantation. Recently, proof-of-principle studies demonstrated that a type I allergic immune response can be durably tolerized by transplantation of allergen-expressing syngeneic bone marrow. We review the concept of tolerance induction through chimerism and discuss the potential of this strategy in immunoglobulin-E-mediated allergy.