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OBJECTIVE: To assess the prognostic value of various parameters including positron emission tomography / computed tomography (PET/CT) and identify risk factors for survival of patients with non-Hodgkin’s lymphoma (NHL) and Hodgkin’s lymphoma (HL) treated with autologous stem cell transplantation (ASCT). METHODS: Patient charts and our prospective ASCT database were assessed for the impact of documented variables on event free survival (EFS) and overall survival (OS), including salvage and conditioning regimens used, and PET/CT results before and after ASCT. RESULTS: Overall, 180 patients with NHL (n = 134; 74%) or HL (n = 46; 26%) received ASCT from December 2000 to May 2011. Of the NHL patients, 59 (44%) had diffuse large B-cell lymphoma (DLBCL). Conditioning was mainly performed with cyclophosphamide, carmustine, etoposide (CBV) (n = 72; 40%) or carmustine, etoposide, cytarabine, melphalan (BEAM) (n = 103; 57%). Treatment-related mortality (TRM) was 1.7%. Outcome data are in line with previously reported studies, especially the data for salvage treatment and BEAM conditioning in DLBCL patients confirmed the outcome reported recently in a phase III study. Positive pre- and post-transplantation PET/CT was an adverse risk factor for survival (PET/CT+ before ASCT: hazard ratio (HR): 2.65 (1.11−6.33), p = 0.029; PET/CT+ after ASCT: HR: 7.11 (2.76−18.34), p <0.0001). Other risk factors for survival were primary refractory disease, initial lymphoma stage, number of previous chemotherapy lines, and high amounts of blood product transfusions. CONCLUSIONS: Conditioning with CBV or BEAM and subsequent ASCT was feasible and effective. Initial lymphoma stage and number of previous treatment lines were identified as independent risk factors for EFS in DLBCL and HL patients.