Purpose To evaluate viscous energy loss and the association with three-dimensional (3D) vortex ring formation in left ventricular (LV) blood flow during diastolic filling. Theory and Methods Thirty healthy volunteers were compared with 32 patients with corrected atrioventricular septal defect as unnatural mitral valve morphology and inflow are common in these patients. 4DFlow MRI was acquired from which 3D vortex ring formation was identified in LV blood flow at peak early (E)-filling and late (A)-filling and characterized by its presence/absence, orientation, and position from the lateral wall. Viscous energy loss was computed over E-filling, A-filling, and complete diastole using the Navier-Stokes energy equations. Results Compared with healthy volunteers, viscous energy loss was significantly elevated in patients with disturbed vortex ring formation as characterized by a significantly inclined orientation and/or position closer to the lateral wall. Highest viscous energy loss was found in patients without a ring-shaped vortex during E-filling (on average more than double compared with patients with ring-shape vortex, P < 0.003). Altered A-filling vortex ring formation was associated with significant increase in total viscous energy loss over diastole even in the presence of normal E-filling vortex ring. Conclusion Altered vortex ring formation during LV filling is associated with increased viscous energy loss. Magn Reson Med 77:794–805, 2017. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.