Objectives: The aim of this study was to assess the commissural alignment between bioprosthetic and native aortic valve leaflets following surgical aortic valve replacement (SAVR) and transcatheter aortic valve replacement (TAVR) and to investigate its impact on valvular function and coronary filling. Background: Expansion and geometry have been shown to affect leaflets of implanted transcatheter aortic bioprosthesis, but commissural alignment has not been studied. Methods: Pre- and post-procedural multidetector computed tomography (MDCT) of 28 SAVR patients and 212 TAVR patients were analyzed. Commissural alignment between the bioprosthetic (post) and native (pre) aortic valves was categorized as aligned (0° to 15° angle deviation) or as mild (15° to 30°), moderate (30° to 45°), or severe (45° to 60°) commissural misalignment (CMA). Results: With SAVR, 27 of 28 cases (96%) were aligned and 1 had mild CMA. For all types of transcatheter heart valves (THVs), there was random valve implantation with regard to commissural alignment: 22% of THVs were aligned, 25% had mild CMA, 22% had moderate CMA, and 31% had severe CMA. The degree of commissural alignment was not associated with a difference in transvalvular gradient, paravalvular aortic regurgitation, or simulated coronary filling. However, there was a significantly higher rate of mild central aortic regurgitation in those THVs with moderate or greater CMA compared with those THV with mild or less CMA (7.8% vs. 1.1%; p = 0.03). Conclusions: Commissural alignment is excellent in case of SAVR but random in case of TAVR. There is no association between CMA and transvalvular gradient or coronary filling; however, there is a significantly higher rate of mild central aortic regurgitation in case of moderate or greater CMA.