Whipple´s disease is a rare multisystem condition affecting < 1/1.000.000 per year. The condition often presents with polyarthritis, diarrhea, and intestinal malabsorption. Endocarditis is seen in a minority of these patients, and is typically culture negative, as the causative agent Tropheryma whipplei does not grow in ordinary culture media. We present the case of a 78-year-old man with a history of seronegative polyarthritis that was refractory to treatment with several biological agents for a duration of 5 years prior to presentation to the emergency department with stroke. Echocardiography revealed aortic valve endocarditis with a 3.6 cm vegetation and multiple smaller vegetations. The patient underwent surgery with aortic valve replacement followed by prolonged antibiotic treatment. 16 S rDNA PCR analysis of the resected valve revealed T. whipplei as the causative agent. Two years after surgery and treatment with antibiotics, the patient's previously longstanding arthritis had totally disappeared and all rheumatological treatment had been discontinued.