A case of blood culture-negative aortic and mitral valve infective endocarditis caused by the bacterium Tropheryma whipplei is reported. A 33-year-old man showed no clinical manifestations of Whipple's disease, with the exception of arthralgia as given in his history. The disease was complicated by recurrent cerebral and left upper limb embolization of vegetations. The causative agent was detected in a valve sample using broad-range polymerase chain reaction. The patient underwent successful surgery (aortic and mitral valve replacement) and his clinical condition during six-month antibiotic therapy was good.