Sterile blood cultures are noted in one third of patients with infectious endocarditis. Although in half of cases this is due to previous antibiotic therapy, in the other half, the aetiology of culture-negative endocarditis is intracellular bacteria such as Coxiella burnetii or fastidious growing bacteria. Although it was previously considered that the prevalence of such organisms was identical throughout the world, recent investigations on Bartonella endocarditis clearly showed that the aetiology of culture-negative endocarditis is likely to be strongly related to epidemiology of the agent in each country. During the past decade the use of molecular techniques such as PCR with subsequent sequencing to detect or to identify bacteria in valves from patients with infectious endocarditis have considerably improved the aetiological diagnosis. This is especially true in the case of culture-negative endocarditis following earlier antibiotic therapy. However, the fact that DNA remnants of past endocarditis can be detected some time after the acute episode, when the patient has been cured, suggests that the predictive value of these techniques along with the traditional histology and culture need to be evaluated closely.