A higher incidence of conduction disturbances and permanent pacemaker implantation (PPI) has been observed after transcatheter aortic valve implantation (TAVI) in patients with bicuspid aortic valves (BAVs) as compared to those with tricuspid aortic valves (TAVs). This study aimed to provide an anatomical explanation for this observation, supported by an in-depth anatomical mapping of the membranous septum (MS) in a large cohort of BAVs and TAVs using cardiac computed tomography (CT). A total of 300 cardiac CT scans were analysed, revealing a significantly shorter sub-annular length of the MS in BAVs at all measuring points compared to TAVs (p < 0.001). In the current BAV cohort, the MS was found to be at its shortest at the RCC site, measuring less than 1 mm in depth. In addition, the MS was located more anteriorly towards the RCC in BAVs, where the transcatheter aortic valve tends to be implanted deeper, and we observed a trend towards a higher PPI rate in BAVs. Future studies should investigate whether anatomical mapping of the MS in patients undergoing TAVI could be a useful tool for decision-making and potentially mitigate the risk of conduction disturbances.