Background Recently, bicuspid aortic valve disease is posed to be a possible risk factor for dilatation of the pulmonary autograft. Methods Analysis of all 123 patients in our prospective cohort with their native aortic valve in situ at the autograft procedure. Results The bicuspid aortic valve group (n = 81) had more males ( p = 0.05), prior cardiac surgery ( p = 0.02), prior aortic valve balloon dilatation ( p = 0.01), aortic stenosis ( p = 0.03), and less deterioration of left ventricular function ( p = 0.02) than the tricuspid group (n = 42). Hospital mortality occurred in 3 patients (bicuspid 2, tricuspid 1). The follow-up was 99% complete (median, 5.3 years; SD, 3.5; range, 0.1 to 13.4) with a total of 674 patient years. During follow-up 4 patients died (bicuspid 2, tricuspid 2). Overall survival was 95% (95% confidence interval [CI], 89% to 98%) at 5 and 10 years. Seven patients required reoperation for autograft failure, all structural. Freedom from autograft reintervention was 97% (95% CI, 92% to 100%) at 5 years and 89% (95% CI, 79% to 98%) at 10 years. There were no differences in outcome between the groups. Four patients required reoperation for allograft failure, all structural. Freedom from allograft reoperation was 99% (95% CI, 97% to 100%) at 5 years and 91% (95% CI, 82% to 100%) at 10 years. There was no difference between the groups. Conclusions An autograft procedure in patients with a bicuspid aortic valve is justified. Bicuspid aortic valve disease is not a contraindication for an autograft procedure. Patients with a bicuspid aortic valve will meet the limitations of the autograft procedure in the same frequency as the overall autograft population.