Juvenile dermatomyositis (JDM) is a chronic inflammatory disorder of unknown aetiology that affects muscle and skin. We report on two patients with severe progressive JDM who developed contractures and were wheelchair dependent despite therapy including methotrexate (MTX), steroids, immunoglobulins, cyclosporin A, and rituximab. On account of the refractory disease, autologous stem cell transplantation (ASCT) was performed using a CD3/CD19-depleted graft after immunoablative conditioning with fludarabine, cyclophosphamide, and anti-thymocyte globulin. This induced a dramatic improvement and sustained remission of the disease in both patients. We demonstrate that ASCT is a therapeutic option with low toxicity for patients with severe, refractory JDM.