A new method for quantifying the transvalvular flow through the mitral valve (MV) based on three-directional velocity-encoded magnetic resonance imaging (MRI) is presented. For thirty time phases during one cardiac cycle, the three-dimensional (3D) velocity vector field of the blood flow is reconstructed from the MRI measurement. Retrospectively, for each time phase, the MV-plane is indicated manually in the velocity data and the flow through this plane is determined, representing the MV flow. Measurements are performed in 10 healthy volunteers. The new method is compared to the conventional, one-directional velocity-encoded MRI method for which an acquisition plane is positioned at the mitral valve at end-systole and remains fixed during the acquisition. The flow measurements with the new method correlate very well with the flow measured in the aorta (r(p)=0.92, p<0.01), whereas the conventional method shows no statistically significant correlation (r(p)=0.15, p=0.68). The low differences between the flow measured at the MV and the flow in the aorta proves high accuracy of the new method. Also, the new method shows very low intra- and interobserver variation, proving the high reproducibility. Three-directional velocity-encoded MRI is a patient-friendly and easy-to-use method suitable for quantifying accurately and reproducibly the transvalvular MV flow.