Stem cell transplant (SCT) has long been the standard of care for several hematologic, immunodeficient, and oncologic disorders. Recently, SCT has become an increasingly utilized therapy for refractory autoimmune rheumatologic disorders (ARDs). The efficacy of SCT in ARDs has been attributed to resetting an aberrant immune system either through direct immune replacement with hematopoietic stem cells or through immunomodulation with mesenchymal stem cells. Among ARDs, refractory systemic sclerosis (SSc) and systemic lupus erythematosus (SLE) are the most common indications for SCT. SCT has also been used in refractory rheumatoid arthritis, inflammatory myopathies, antiphospholipid syndrome, granulomatosis with polyangiitis, and pediatric ARDs. Complete responses have been reported in approximately 30 % of patients in all disease categories. Transplant-related mortality, however, remains a concern. Future large multi-center prospective randomized clinical trials will help to better define the specific role of SCT in the treatment of patients with ARDs.