We describe a case of Q-fever endocarditis with severe destruction of the aortic valve with perivalvular abscess formation and cardiac failure. The patient needed urgent operative treatment and postoperative critical care. All specimens sent for microbiological examination were negative. Molecular analysis, including fluorescence in situ hybridization of aortic valve tissue combined with PCR and sequencing, led to the correct diagnosis and to appropriate anti-infective treatment. The patient subsequently recovered from complex cardiovascular surgery. This is the first report on Q-fever endocarditis that was rapidly diagnosed using these methods.