The success of marrow or blood stem cell transplantation may depend upon events arising months to years later. Transplant regimen related toxicity may include cataract formation due to corticosteroids or total body irradiation (TBI) and endocrine or gonadal dysfunction requiring hormonal replacement. By 15 to 20 years post-transplant, the cumulative incidence of secondary malignancies (including skin cancers) ranges from 4% (no TBI) to 14% (prior irradiation) in patients with previous aplastic anemia. Chronic graft versus-host-disease (GVHD) develops in 33% of HLA-identical sibling transplants and requires 1 to 2 years of immunosuppressive therapy. In allograft recipients free of GVHD, there are very few late infections or complications. These findings are confirmed by multidimensional studies of the quality of life of adult patients surviving 6 to 18 years after marrow transplantation and demonstrate that 80% of patients rate their quality of life as good to excellent and 5%, as poor. Considerations of late effects of transplant and maintenance of quality of life are key considerations when weighing the risks and benefits of stem cell grafts for the treatment of severe autoimmune diseases. Careful followup and reporting of these initial patient cohorts will be vital in determining the longterm success of stem cell transplantation.