The authors describe the presentday possibilities of routine and molecular microbiologic diagnostics of infective endocarditis (IE). Routine diagnostics employs automated microbial growth and biochemical detection systems. Molecular methods are based on polymerase chain reaction (PCR) and matrix assisted laser desorption/ ionization time of flight mass spectrometry (MALDI-TOF MS). MALDI-TOF MS first appeared in the new guidelines for the management of IE of the European Society of Cardiology published in 2015. The greatest benefit of MALDITOF MS is the short time of pathogen identification. The main disadvantages are the necessity of routine agar cultures and lack of antimicrobial susceptibility estimation. So far, there has been no Polish literature report on MALDI-TOF MS used for pathogen identification in suspected IE. This may well result from scarce accessibility of the method in Poland. The paper aims to stress the importance of an up-todate technology in the diagnostics of difficult, blood culture negative cases of IE. It also takes into consideration the limitations of mass spectrometry in the ESC diagnostic scheme of IE.