The role of procalcitonin (PCT) in the diagnosis of infective endocarditis (IE) remains unclear. The aim of our study was to test the accuracy of PCT in the early diagnosis of IE and analyse if the accuracy of PCT is dependent on the type of pathogen causing IE. We carried out a prospective analysis of hospitalised patients referred for transthoracic echocardiography to search for an IE. The plasma PCT value was measured at the time of echocardiography. The diagnosis of IE was made using the modified Duke criteria. A total of 77 patients were included. IE was confirmed in 15 patients. The mean PCT values were 6.9 (+/-21.6) ug/l in patients without IE and 6.4 (+/-11.7) ug/l in patients with confirmed IE (p=0.92). IE patients with Staphylococcus aureus bacteraemia (n=7) had significantly higher PCT values compared to IE patients with other types of bacteraemia (n=8) (13.1 vs. 0.435, p=0.0299). This study demonstrates that PCT levels markedly differ at the time when IE is diagnosed. While PCT values are very high in patients with S. aureus bacteraemia, they are surprisingly low in patients with Streptococcus viridans bacteraemia, which are common offenders of endocarditis. We conclude that serum PCT has the potential to be used in the early diagnosis of S. aureus endocarditis.