In the submitted case-history the authors describe autologous haematopoietic stem cell transplantation (ASCT) in a patient suffering from juvenile chronic arthritis (JCA). ASCT was indicated by rheumatologists and haematologists for refractory polyarticular JCA. Mobilization with cyclophosphamide and granulocyte-colony stimulating factor was effective in terms of CD34+ cell shift to peripheral blood and the good quality autograft reliably led to haematopoetic recovery after megachemotherapy. The peritransplant period was not complicated with life threatening events. Immunosuppressive effect of autotransplant has reduced signs of rheumatoid disease activity and enabled conventional drug dose reduction. Autotransplant of haematopoietic stem cells has a potential to reduce activity of juvenile chronic arthritis.