This study was intended to evaluate the diagnostic value of three dimensional proximal isovelocity surface area (3D PISA) derived effective regurgitant orifice area (EROA) and the accuracy of automatic 3D PISA detection in a population resembling clinical practice. Quantification of mitral regurgitation (MR) remains challenging and 3D PISA EROA is a novel diagnostic tool with promising results. However its’ usefulness compared to guideline endorsed parameters has not been shown. In 93 consecutive patients examined in routine practice conventional parameters and 3D-datasets for offline 3D PISA evaluation were recorded. EROA was determined from the largest (peak) PISA and also averaged over systole for meanEROA. Results of 3D PISA calculation were compared with a combination of expert grading by two examiners and two scores for MR grading. In receiver operator characteristic-analysis the meanEROA as determined by 3D PISA had the best diagnostic value (AUC = 0.907 CI 0.832–0.983) as compared to peakEROA (AUC 0.840 CI 0.739–0.941), vena contracta width (AUC 0.831 CI 0.745–0.918) and 2D PISA (AUC 0.747 CI 0.644–0.850). A meanEROA of 0.15 cm² had a sensitivity of 88.2 % and a specificity of 81.4 % for distinguishing severe from non-severe MR. Semiautomatic 3D PISA detection correlated very well with manually corrected values (r = 0.955). Semiautomatic 3D PISA measurement is feasible in a clinical population and has better diagnostic value compared to 2D PISA. Calculation of mean EROA throughout systole further improves diagnostic value compared to conventional parameters.