Background: The objective of this study is to investigate clinical outcomes in patients with bicuspid aortic valves (BAV) after surgical treatment for endocarditis. Methods: This was a population-based, observational cohort study, conducted on all patients who received aortic valve surgery for native or prosthetic valve endocarditis at Karolinska University Hospital between 2002-2020. Baseline characteristics and postoperative complications were collected from the institutional surgical database and patient medical charts. The primary endpoint was all- cause mortality. We used unadjusted and adjusted Cox regression to determine the association between valve morphology and longterm mortality. Results: Of the 338 patients, 122 (36%) had a BAV and 216 (64%) had a tricuspid aortic valve (TAV). The mean follow-up was 5.8 years (maximum 18.4 years). Survival rates at one, five, ten and 14 years were 88%, 81%, 78% and 76% versus 85%, 69%, 58% and 43%, in BAV and TAV patients, respectively [adjusted hazard ratio (HR) 0.64; 95% confidence interval (CI): 0.39-1.05]. In patients with native valve endocarditis, those with BAV had lower all-cause mortality compared to those with TAV (adjusted HR 0.44; 95% CI: 0.22-0.89), despite having a higher prevalence of perivalvular abscess (40% versus 22%, respectively, in BAV and TAV patients). In patients with prosthetic valve endocarditis, original valve morphology did not affect all-cause mortality (adjusted HR 1.94; 95% CI: 0.64-5.87). Conclusions: In patients with native valve endocarditis, a BAV was associated with improved survival after surgical treatment. In patients with prosthetic valve endocarditis, survival was not affected by the original valve morphology of the patient.