Salvage reinduction therapy followed by high-dose chemotherapy (HDCT) and auto-SCT is the treatment of choice for fit patients with refractory or relapsed aggressive non-Hodgkin's lymphoma (NHL). We assessed the prognostic value of comorbidity at the time of relapse to predict receipt of auto-SCT and outcome. We analyzed 156 consecutive NHL patients, referred to our center between 1999 and 2007 for salvage reinduction therapy, followed by HDCT and auto-SCT. Comorbidity according to the hematopoietic SCT comorbidity index was scored at relapse and directly before HDCT and auto-SCT. Primary end points were actual receipt of auto-SCT and survival. At relapse, comorbidity scores of 0, 1-2 and X3 were found among 64 (41%), 62 (40%) and 30 (19%) patients, respectively. Ultimately, 95 patients received auto-SCT. Higher comorbidity scores at relapse were associated with significantly less chance of receiving auto-SCT and with inferior OS, independently from secondary age-adjusted International Prognostic Index (sAAIPI) scores. For transplanted patients, OS rates at 5 years were 62, 30 and 17% for relapse comorbidity scores of 0, 1-2 and X3, respectively. In patients with relapsed NHL, comorbidity at relapse is associated with receipt of auto-SCT and subsequent survival independently from the sAAIPI.