We report a case of Q fever endocarditis, with cross-reactive serology, where serum polymerase chain reaction was useful to make the diagnosis. Although serodiagnostics are the reference standard, they have limitations. They cross-react with related bacterial species and are not useful in anatomically localizing the infection. Serum polymerase chain reaction may play a promising role in the diagnosis of Q fever, especially endocarditis. Q fever should be considered in the differential diagnosis of culture-negative endocarditis in the United States.