Current epidemiological trends of infective endocarditis (IE) in Greece were investigated via a prospective cohort study of all cases of IE that fulfilled the Duke criteria during 2000-2004 in 14 tertiary and six general hospitals in the metropolitan area of Athens. Demographics, clinical data and outcome were compared for nosocomial IE (NIE) and community-acquired IE (CIE). NIE accounted for 42 (21.5%) and CIE for 153 (78.5%) of 195 cases. Intravenous drug use was associated exclusively with CIE, while co-morbidities (cardiovascular disease, diabetes mellitus, chronic renal failure requiring haemodialysis and malignancies) were more frequent in the NIE group (p <0.05). Prosthetic valve endocarditis (PVE) predominated in the NIE group (p 0.006), and >50% of NIE cases had a history of vascular intervention. Coagulase-negative staphylococci and enterococci were more frequent in cases of NIE than in cases of CIE (26.2% vs. 5.2%, p <0.01, and 30.9% vs. 16.3%, p 0.05, respectively). Enterococci accounted for 19.5% of total IE cases and were the leading cause of NIE. Staphylococcus aureus IE was hospital-acquired in only 11.9% of cases. In-hospital mortality was higher for NIE than for CIE (39.5% vs. 18.6%, p 0.02). Cardiac failure (New York Heart Association grade III-IV; OR 13.3, 95% CI 4.9-36.1, p <0.001) and prosthetic valve endocarditis (OR 3.7, 95% CI 1.3-10.6, p 0.01) were the most important predictors of mortality.