Background: The area of the left ventricular outflow tract (ALVOT) represents a major component of the continuity equation (CE), which is, i.a., crucial to calculate the aortic valve (AV) area (AAV). The ALVOT is typically calculated using 2D echo assessments as the measured anterior–posterior (a/p) extension, assuming a round LVOT base. Anatomically, however, usually an elliptical shape of the LVOT base is present, with the long diameter extending from the medial–lateral axis (m/l), which is not recognized by two-dimensional (2D) echocardiography. Objective: We aimed to compare standard and three-dimensional (3D)-echocardiography-derived ALVOT calculation and its use in a standard CE (CEstd) and a modified CE (CEmod) to calculate the AAV vs. computed tomography (CT) multi-planar reconstruction (MPR) measurements of the anatomical ALVOT, and AAV, respectively. Methods: Patients were selected if 3D transthoracic echocardiography (TTE), 3D transesophageal echocardiography (TEE), and cardiac CT were all performed, and imaging quality was adequate. The ALVOT was assessed using 2D calculation, (a/p only), 3D-volume MPR, and 3D-biplane calculation (a/p and m/l). AAV was measured using both CEstd and CEmod, and 3D-volume MPR. Data were compared to corresponding CT analyses. Results: From 2017 to 2018, 107 consecutive patients with complete and adequate imaging data were included. The calculated ALVOT was smaller when assessed by 2D- compared to both 3D-volume MPR and 3D-biplane calculation. Calculated AAV was correspondingly smaller in CEstd compared to CEmod or 3D-volume MPR. The ALVOT and AAV, using data from 3D echocardiography, highly correlated and were congruent with corresponding measurements in CT. Conclusion: Due to the elliptic shape of the LVOT, use of measurements and calculations based on 2D echocardiography systematically underestimates the ALVOT and dependent areas, such as the AAV. Anatomically correct assessment can be achieved using 3D echocardiography and adapted calculations, such as CEmod.