Abstract Background Computational fluid dynamics (CFD), which has the advantages of providing detailed pressure distribution, has been widely used for cardiac function assessment and heart disease diagnosis. However, the results are usually influenced by the boundary conditions. Particularly, the transvalvular pressure gradient, which serves as a crucial indicator for mitral stenosis and the efficacy of mitral valve surgery, can easily be miscalculated. Here, we assess the effects of widely used boundary conditions on the transvalvular pressure gradient computed based on the Bernoulli equation and the line probe, respectively. Purpose This study aims to determine the effects of boundary conditions on the transvalvular pressure gradient in CFD. Methods We constructed cardiac models including left atrium, left ventricle, aorta from CT and mitral valve from transesophageal echocardiography data (Figure 1). The intraventricular flow fields were computed using CFD tool with four different boundary conditions (BC) at the same cardiac output. BC1 involved specifying the total flow rate of the aorta, with zero pressure at the entrance of the pulmonary veins. BC2 maintained equal flow rates at the entrances of the pulmonary veins. BC3 followed Murray's law, where the flow rate ratio in the pulmonary veins is proportional to the 1.5 power of the area ratio. BC4 followed Poiseuille's law, where the flow rate ratio is proportional to the square of the area ratio. The results encompassed the mean transvalvular pressure gradient and peak transvalvular pressure gradient obtained through the Bernoulli equation and the line probe methods, respectively. Results Figures 2(A-D) present the contours of transvalvular pressure under peak flow velocity conditions and the isosurfaces of vorticity within the ventricle. The results show that the pressure within the atrium is notably lower in the BC2, leading to a 63% underestimation in the mean transvalvular pressure gradient and a 22.9% deviation in the peak transvalvular pressure gradient (Figure 2 F). The transvalvular pressure gradient for BC1, BC3, and BC4 do not exceed 10%. The results reveal that the pressure distribution and vorticity within the ventricle are consistent, primarily due to the influence of the mitral valve. Conclusion When evaluating transvalvular pressure gradient using CFD, it is crucial to specify appropriate boundary conditions. Using inappropriate boundary conditions may lead to underestimation of the transvalvular pressure gradient, thereby affecting further diagnostic decisions. In research studies, it is recommended to allocate flow in different branch vessels according to Murray's law, where the flow in different branch vessels is proportional to the 1.5 power of the vessel cross-sectional area.Modelling flow chartTransvalvular pressure gradient