Infectious endocarditis remains both a diagnostic and a treatment challenge. A positive outcome depends on a rapid diagnosis, accurate risk stratification, and a thorough follow-up. Imaging plays a key role in each of these steps and echocardiography remains the cornerstone of the methods in use. The technique of both transthoracic echocardiography and transoesophageal echocardiography has been markedly improved across the last decades and most recently three-dimensional real-time echocardiography has been introduced in the management of endocarditis patients. Echocardiography depicts structural changes and abnormalities in the heart, but it does not uncover the underlying pathophysiological processes at the cellular or molecular level. This problem is addressed with introduction of new molecular imaging methods as (18)F-fluorodesoxyglucose ((18)F-FDG) PET-CT and single photon emission computed tomography fused with conventional CT (SPECT/CT). Of these methods, (18)F-FDG PET-CT carries the best promise for a future role in endocarditis. But there are distinct limitations with both SPECT/CT and (18)F-FDG PET-CT which should not be neglected. MRI and spiral CT are methods primarily used in the search for extra cardial infectious foci. A flowchart for the use of imaging in both left-sided and right-sided endocarditis is suggested.