Infective endocarditis is associated with significant morbidity and mortality, with valvular destruction and congestive heart failure being more common in patients with echocardiographically discernible vegetations. The transoesophageal approach affords consistently high quality images with excellent structural resolution. Two-hundred and eighty-one patients with clinically suspected infective endocarditis were studied, to evaluate the prognostic value of ascertaining the site of vegetations. Among them were 118 patients with vegetations attached to the aortic or mitral valve. These patients were followed for a mean period of 14 months. Mitral valve vegetations were associated with a significantly higher incidence of embolic events than vegetations on aortic valves (25% vs 9.7%). The incidence of abscess formation was higher in aortic than in mitral valve endocarditis (6% vs 0%), as were the need for surgical intervention (11% vs 5.5%) and mortality (1.6% vs 0%) respectively). Bivalvular endocarditis was associated with an increased rate of complications: embolism (50%), abscess formation (15%), surgery (35%) and mortality (10%). By multivariate analysis, echocardiographically accessible risk factors for subsequent embolism were a vegetation size of more than 10 mm and mitral valve involvement. Risk factors associated with in-hospital fatality were embolism, a vegetation size of more than 10 mm, and Staphylococcus aureus infection. Our data suggest that the site influences both the rate and the type of complications. Precise echocardiographic visualization of vegetations helps to stratify patients into a high-risk sub-group, perhaps warranting early prophylactic surgical intervention. Transoesophageal echocardiography may play an important role in assessing the clinical outcome for these patients.