Abstract Background Four-dimensional cardiovascular magnetic resonance (CMR) flow assessment (4D flow) allows to derive volumetric quantitative parameters in mitral regurgitation (MR) using retrospective valve tracking. However, prior studies have been conducted in functional MR or in patients with congenital heart disease, thus, data regarding the usefulness of 4D flow CMR in case of a valve pathology like mitral valve prolapse (MVP) are scarce. This study aimed to evaluate the clinical utility of cine-guided valve segmentation of 4D flow CMR in assessment of MR in MVP when compared to standardized routine CMR and transthoracic echocardiography (TTE). Methods Six healthy subjects and 54 patients (55 ± 16 years; 47 men) with MVP were studied. TTE severity grading used a multiparametric approach resulting in mild/mild-moderate (n = 12), moderate-severe (n = 12), and severe MR (n = 30). Regurgitant volume (RVol) and regurgitant fraction (RF) were also derived using standard volumetric CMR and 4D flow CMR datasets with direct measurement of regurgitant flow (4DFdirect) and indirect calculation using the formula: mitral valve forward flow - left ventricular outflow tract stroke volume (4DFindirect). Results There was moderate to strong correlation between methods (r = 0.59–0.84, p