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Aortic valve endocarditis might be the first manifestation of Whipple’s disease without further multiorgan involvement. A case is reported of aortic valve endocarditis with severe aortic regurgitation without clinical evidence of gastrointestinal disease in a 47 year old man who was admitted because of increasing dyspnoea and fatigue. During the patient’s stay in hospital, infection parameters were rising while blood cultures remained negative. Multiplane three dimensional transoesophageal echocardiography showed increased end diastolic and end systolic diameters (72/57 mm) with left ventricular dysfunction, enlarged atria, satellite vegetations on the anterior mitral valve leaflet and associated chordae, slight mitral regurgitation, and a flail aortic valve with vegetations on all coronary cusps, as well as a cusp perforation of the left coronary cusp, which was diagnosed by three dimensional reconstruction. The cusp perforation of the left coronary cusp is clearly visible as a black hole. The deformities caused by vegetations on the right coronary cusp (rc), non-coronary cusp (nc), and left coronary cusp (lc) are also evident (RA, right atrium; LA, left atrium; RCA, right coronary artery; LCA, left coronary artery). The diagnosis of aortic valve endocarditis caused byTropheryma whippelii was made after aortic valve replacement, using polymerase chain reaction of the aortic valve remnants and confirmed by DNA sequence analysis.