The aims of this study are to estimate the incidence, the outcome and the associated risk factors of infective and non-infective endocarditis (IE and NIE, respectively) in intensive care unit (ICU) patients. We studied the post-mortem findings and the clinical data of the patients who died in our ICU between 1996 and 2010. Of the 765 reviewed autopsies, 21 patients (2.7%) presented cardiac vegetations. These cases consisted of 12 IEs and 9 NIEs. Three patients with IE had a mechanical prosthetic valve, and in 11 cases invasive devices had been used. Multiple peripheral embolisms were discovered at autopsy. In particular, the brain appeared to be more affected in patients with IE, while pulmonary embolisms were commonly associated with NIE. Blood cultures were positive in nine patients with IE. The imaging diagnostics (transthoracic and transesophageal echocardiography) which were seldom performed in both groups, proved to be of little help. As a consequence, an IE was correctly diagnosed before death in three patients (25%) and suspected in two other cases (17%), while a NIE was diagnosed before death in one patient alone. In conclusions, critically ill patients admitted to general ICUs, multiple factors related both to the underlying conditions and to performed procedures can facilitate the occurrence of IE and NIE making, at the same time, their diagnosis challenging. Many cases, in fact, are diagnosed only at autopsy. Yet again, post-mortem examination proves to be an invaluable tool for the evaluation of diagnostic accuracy in critical care.