The results of experiments with the induced autoimmune diseases adjuvant arthritis and allergic encephalomyelitis in rats, which led to the discovery of the curative effect of autologous bone marrow transplantation following high-dose myeloablative treatment, are reviewed. The rationale is eradication of the autoreactive lymphocytes and memory cells, and the prevention of relapse due to transfer of lymphocytes with the autograft. Comparison of various conditioning regimens in the animal models indicates that a combination conditioning with low-dose total body irradiation (TBI) and high-dose cyclophosphamide is optimal. These findings were the basis for the conditioning currently employed in the treatment of polyarticular juvenile chronic arthritis (JCA) by the teams in Utrecht and Leiden, which consists of cyclophosphamide 50 mg/kg for 4 days, 4 Gy TBI and anti-thymocyte globulin (ATG). The use of TBI for the treatment of non-malignant disease is regarded as undesirable by many physicians in view of the risks, in particular, of growth inhibition in children and the induction of tumours. Experimental and clinical data show that a dose of 4 Gy does not cause significant inhibition of skeletal growth in infants. The risk of excess cancer due to TBI has been well established in quantitative terms and is compared with the expected risk of high-dose cyclophosphamide and the risk associated with the highly immunosuppressive regimens currently used for the treatment of JCA.