Three randomized controlled trials in early severe systemic sclerosis demonstrated that autologous hematopoietic stem cell transplantation was superior to standard cyclophosphamide therapy. This European Society for Blood and Marrow Transplantation multicenter, prospective, non-interventional study was designed to further decipher efficacy and safety of this procedure for severe systemic sclerosis patients in real-life practice and to search for prognostic factors. All consecutive adult patients with systemic sclerosis undergoing a first autologous hematopoietic stem cell transplant between December 2012 and February 2016 were prospectively included in the study. The primary endpoint was progression-free survival. Secondary endpoints were overall survival, non-relapse mortality, response and incidence of progression. Eighty patients with systemic sclerosis were included. The median duration of the follow-up was 24 (range, 6-57) months after stem cell transplantation using cyclophosphamide plus antithymocyte globulin conditioning for all, with CD34+ selection in 35 patients. At 2 years, the progression- free survival rate was 81.8%, the overall survival rate was 90%, the response rate was 88.7% and the incidence of progression was 11.9%. The 100-day non-relapse mortality rate was 6.25% (n=5) with four deaths from cardiac events, including three due to cyclophosphamide toxicity. Modified Rodnan skin score and forced vital capacity improved with time ( P<0.001). By multivariate analysis, baseline skin score >24 and older age at transplantation were associated with lower progression-free survival (hazard ratios 3.32 and 1.77, respectively). CD34+-cell selection was associated with better response (hazard ratio 0.46). This study confirms the efficacy of autologous stem cell transplantation, using nonmyeloablative conditioning, in real-life practice for severe systemic sclerosis. Careful cardio-pulmonary assessment to identify organ involvement at the time of the patient’s referral, reduced cyclophosphamide doses and CD34+-cell selection may improve outcomes. The study was registered at ClinicalTrials.gov: NCT02516124.