A case of Q fever endocarditis was diagnosed in a patient with no sign of active endocarditis by performing PCR targeting eubacterial 16S rDNA on the resected mitral valve. The diagnosis was confirmed by detection of high levels of anti-Coxiella burnetti antibodies, positive immunohistologic analysis of the valve tissue with specific antibodies and culture of C. burnetti from the valve tissue. As this patient had an unexplained aggravation of valve dysfunction, we recommended routine serologic testing for C. burnetti to allow the diagnosis of Q fever endocarditis at a very early stage.