The aim of this study was to analyse flow characteristics of two different prosthetic valves by means of a non-invasive 3D Doppler technique. As previously demonstrated, negative velocity peaks within a 3D-Doppler profile significantly correlate with the severity of aortic stenosis. Transesophageal echocardiography was performed in 42 patients with normal aortic valves and in 35 patients after aortic valve replacement (bileaflet n=23, tilting-disc n=12). Three-dimensional reconstruction of color Doppler data was performed by the EchoAnalyzer software developed at our institution. Cross-section velocity distribution in the ascending aorta was analysed 2 cm distal to the aortic valve in 3 different sectors (non-coronary (NC), left-coronary (LC) or right-coronary (RC)). The percentages of negative velocity values (PNVV) in native aortic valves (6.8+/-6.4%, range: 0-21.8%) were significantly lower (P<0.0001) than in prosthetic valves (bileaflet: 38.5+/-18.5%, range: 13.2-71%; tilting-disc: 47.2+/-17.6%, range: 21.7-78.1%). Significant differences between normal and prosthetic valves were found in all different sectors. Furthermore, Medtronic Hall showed significantly higher PNVV than St. Jude Medical within the LC sector (P=0.03). This method, which allows non-invasive analysis of 3D flow distributions in patients, revealed significant differences between prosthetic valves and native valves as well as among different prosthetic types.