We estimated the prevalence of blood culture negative endocarditis (CNE) and described and analysed data with special attention to antibiotic treatment from patients with infective endocarditis (IE) reported to the Swedish endocarditis registry during the 10-y period 1995-2004. All 29 departments of infectious diseases in Sweden reported data to the registry. During the 10-y period, 2509 IE episodes (78% Duke definite) were identified in 2410 patients. 304 CNE episodes (25% Duke definite) were found. The proportion of CNE was measured to be 12% of all IE episodes. Fatal outcome occurred in 10.7% of all IE patients and in 5% of the CNE patients. The risk of dying was significantly increased in female (9%) compared to male (2%) CNE patients (OR 5.1). Mortality was significantly decreased in patients treated with an aminoglycoside (3%) versus patients without aminoglycoside therapy (13%), OR 0.2. In conclusion, the prevalence of CNE was 12% in Swedish IE patients in a 10-y survey. The mortality in IE was low (10.7%) and 4.6% for CNE. Women have higher mortality rates than men in CNE. CNE patients who received aminoglycoside therapy survived more frequently than CNE patients without this therapy.