Systemic sclerosis is an autoimmune connective tissue disease affecting both skin and internal organs. Progressive disease with multiple organ involvement is considered to have a poor prognosis. Treatment possibilities are limited, but certain patients may benefit from autologous hematopoietic stem cell transplantation (auto-HSCT). We report a case of a 30-year-old woman with progressive diffuse systemic sclerosis treated with parenteral cyclophosphamide with unsatisfactory results. Due to progression of the disease and lack of alternative therapies auto-HSCT was performed. After instituting treatment with autologous hematopoietic stem cell transplantation no immunosuppressive therapy has been required during 5-year follow-up. Improvement in exertion tolerance, partial regression of skin lesions and stabilization of pulmonary and cardiovascular changes were observed. Currently therapeutic options in patients with progressive systemic sclerosis are limited. Hematopoietic stem cell transplantation might become an alternative therapeutic solution not only in the early phase of the disease but also among selected patients with progressive systemic sclerosis resistant to standard therapy.