Effective regurgitant orifice area is a useful index of the severity of mitral regurgitation (MR). The calculation of regurgitant orifice area using the proximal isovelocity surface area (PISA) method has some technical limitations. Three-dimensional reconstruction of the MR jet was performed using the Live 3D system on a Sonos 7500 to measure regurgitant orifice area directly in 109 cases of MR. Regurgitant orifice area was also measured by quantitative 2-dimensional echocardiography and by the PISA method. To analyze the shape of the regurgitant orifice, the ratio of the long axis to the short axis of the orifice (the L/S ratio) was calculated. Regurgitant orifice area on 3-dimensional echocardiography showed an almost identical correlation with that obtained by quantitative echocardiography (r = 0.91, p <0.0001, slope = 0.97) regardless of the L/S ratio. It was also significantly correlated with orifice area obtained using the PISA method (r = 0.93, p <0.0001). However, orifice area on 3-dimensional echocardiography was significantly larger than that obtained using the PISA method in the whole study group and in the 62 cases of MR with L/S ratios >1.5, whereas the correlation was almost identical in cases of MR with L/S ratios < or =1.5. Orifice area obtained using the PISA method also underestimated that obtained by quantitative echocardiography in cases of MR with L/S ratios >1.5. Three-dimensional echocardiography provided robust values independent of the eccentricity of the MR jet or of cardiac rhythm. In conclusion, the direct measurement of the regurgitant orifice area of MR with 3-dimensional Doppler echocardiography could be a promising method to overcome the limitations of the PISA method, especially in cases of MR with elliptic orifice shapes.