The current status of stem cell transplantation in rheumatoid arthritis, juvenile chronic arthritis, systemic lupus erythematosus, and systemic sclerosis are reviewed. From a large European bone marrow transplant registry, a birds' eye view of stem cell transplantation for autoimmune disease can be obtained. Among 43 rheumatoid arthritis patients, 35 juvenile chronic arthritis patients, 34 systemic lupus erythematosus patients, and 58 systemic sclerosis patients who underwent stem cell transplantation, initial responses in most patients were good to excellent. Although initial transplant related mortality was low for rheumatoid arthritis, somewhat higher rates for juvenile chronic arthritis, systemic lupus erythematosus, and systemic sclerosis may be falling with modifications in the stem cell transplantation regimens. In rheumatoid arthritis and systemic lupus erythematosus treatment, the criteria for patient selection are still not clear and the therapeutic regimens for stem cell transplantation (and whether follow-up treatment is necessary) are not fully defined. In juvenile chronic arthritis, responses are encouraging although little fully published data beyond that from the European Bone Marrow Transplant Registry exist. In systemic sclerosis, criteria for patient selection and a limited number of stem cell transplantation regimens have been agreed on and controlled trials are underway.