In computed tomography (CT) evaluation prior to transcatheter aortic valve implantation area- and perimeter-based calculation of the aortic annulus diameter, the so-called effective annulus diameter (ED), is the preferred parameter for decision making regarding prosthesis sizes. Currently, it is unclear how relevant the differences between the two methods of measurement are and how they are influenced by the cardiac cycle. The aim of this study was to compare area- and perimeter-based measurements in computed tomography derived aortic annulus sizing. A total of 60 patients who underwent evaluation for transcatheter aortic valve implantation were included in this study. All patients received pre-procedural ECG gated CT. The aortic annulus area and perimeter were measured and the derived ED compared using parametric statistics and Bland and Altman analysis. The mean patient age was 80.2 ± 4 years. Systolic aortic annulus area and perimeter were higher compared to diastolic results (mean difference area 12.8 ± 24 mm² and perimeter 0.72 ± 1 mm; p = 0.009–0.068). Both the area- and perimeter-based ED had a good agreement within two standard deviations for systolic and diastolic measurements. Effective diameter measurements derived from the area were significantly smaller compared to perimeter-based measurements (mean difference: systolic 0.72 ± 0.3 mm and diastolic 0.81 ± 0.4 mm; p < 0.001). While the area-based ED was significantly influenced by the cardiac cycle with a mean difference of 0.4 ± 0.6 mm (p = 0.009), no significant difference was found for the perimeter-based ED (mean difference: 0.2 ± 0.4; p = 0.07). For patients undergoing CT evaluation prior to transcatheter aortic valve implantation, the perimeter-based effective annulus diameter provides a reliable parameter for annulus sizing without significant affection by the cardiac cycle and therefore facilitates annulus measurements with a single heart phase. However, perimeter-based diameters of the annulus are significantly larger than area-based diameters.