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Background: The area of the left ventricular outflow tract (A_LVOT) represents a major component of the continuity equation (CE), which is, i.a., crucial to calculate the aortic valve (AV) area (A_AV). The A_LVOT 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 A_LVOT calculation and its use in a standard CE (CE_std) and a modified CE (CE_mod) to calculate the A_AV vs. computed tomography (CT) multi-planar reconstruction (MPR) measurements of the anatomical A_LVOT, and A_AV, 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 A_LVOT was assessed using 2D calculation, (a/p only), 3D-volume MPR, and 3D-biplane calculation (a/p and m/l). A_AV was measured using both CE_std and CE_mod, 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 A_LVOT was smaller when assessed by 2D- compared to both 3D-volume MPR and 3D-biplane calculation. Calculated A_AV was correspondingly smaller in CE_std compared to CE_mod or 3D-volume MPR. The A_LVOT and A_AV, 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 A_LVOT and dependent areas, such as the A_AV. Anatomically correct assessment can be achieved using 3D echocardiography and adapted calculations, such as CE_mod.