High-dose chemotherapy with autologous stem cell transplantation (SCT) is widely used as a treatment for systemic AL amyloidosis, but its efficacy has not been proved and it has substantial toxicity in this setting. We report here the outcome of 92 patients evaluated at the UK National Amyloidosis Centre who underwent SCT for AL amyloidosis between 1994 and 2004 in various British centres. Median age was 53 years and median of two organs were affected by amyloidosis. All-cause day 100 mortality [treatment-related mortality (TRM)] was 23% for the entire cohort, although this was substantially greater for patients treated from 1994 to 1998 (15/47, 32%) than subsequently (6/45, 13%). Independent factors significantly associated with TRM on multivariate analysis were: number of affected organs, performance status, serum albumin and age. Response of the underlying clonal disease, defined by > or = 50% reduction in the aberrant serum-free light chain concentration, occurred in 83% of evaluable patients. Overall median survival was 5.3 years, and was 8.5 years among patients who survived beyond day 100. Despite recent refinements in patient selection, TRM remains substantial during SCT for systemic AL amyloidosis, and its place in the therapeutic armamentarium for this disease needs to be defined in randomised controlled clinical studies.