Background Surgical intervention for persistent active native aortic valve endocarditis (NVE) remains challenging. We analyzed our combined experience with allografts and mechanical prostheses (MP) in NVE operations. Methods Between 1980 and 2002, 138 patients (81% males) underwent aortic valve replacement for NVE in 2 centers (106 allografts; 32 MPs). Perioperative characteristics and early and late morbidity and mortality were analyzed. Results Mean age was 47 years (range, 14 to 76 years), and 34% required emergency surgery. Abscess rate was 38% for allografts vs 18% for MPs. Concomitant mitral valve replacement was required in 38% MP patients and in 5% allograft patients. Hospital mortality was 8% (n = 11; p = 0.25): 10 allograft patients (9%) and 1 MP patient (3%). During a mean 8-year follow-up (range, 0 to 25 years) 33 patients died: 22 allograft (24%) and 11 MP patients (21%; p = 0.14). Survival at 15 years was 59% ± 6% for allograft patients and 66% ± 9% for MP patients ( p = 0.68). Late recurrent endocarditis developed in 6 allograft patients and 1 MP patient ( p = 0.29). Overall 15-year freedom from reoperation was 76% ± 9% for allografts and 93% ± 6% for MPs ( p = 0.02). Conclusions Mechanical prostheses have comparable rates of midterm survival and freedom from recurrent infection. However, this is in combination with extensive excision of destructive tissue in a specific patient subset. Allograft reoperation rates increase with time. The importance of the mechanical prosthesis in NVE might be established in the coming years.