Aims We analysed the outcome of young adults with congenital aortic valve disease who underwent allograft or autograft aortic valve or root replacement in our institution and evaluated whether there is a preference for either valve substitute. Methods and results Between 1987 and 2007, 169 consecutive patients with congenital aortic valve disease aged 16-55, participating in our ongoing prospective follow-up study, underwent 63 autograft and 106 allograft aortic valve replacements (AVRs). Mean age was 35 years (SD 10.8), 71% were males. Aetiology was 71% bicuspid valve, 14% other congenital, and 15% BV endocarditis. Twenty-two percent underwent previous cardiac surgery; 11% had an ascending aorta aneurysm. Two patients died in hospital. During follow-up six more patients died and 45 patients required valve-related re-operations. Thirteen-year survival was 97% for autograft and 93% for allograft recipients, 13 year freedom from valve-related re-operation was 63% for autograft and 69% for allograft patients. Conclusion In patients with congenital aortic valve disease, autograft and allograft AVR show comparable satisfactory early and long-term results, with the increasing re-operation risk in the second decade after operation remaining a major concern.