Samples from cardiac valves of 31 patients were analyzed by gas chromatography and mass spectrometry. The algorithm of mass spectrometric parameters was developed, which permitted the determination of about 200 known microbial fatty acids, aldehydes and sterols, sufficient for the detection and quantitative determination of more that 170 taxons of clinically significant microorganisms on the genus or species levels. The quantitative and qualitative differences in the composition of microbial markers of endocardial valves in normal and pathological states, particularly in cases of infectious endocarditis, were detected. The participation of 37 microbial taxons in the process was confirmed. The level of endocardium colonization in infectious endocarditis reached from 2 to 7 x 10(9) microbial cells/g of valvular tissue (which exceeded twofold the equivalent concentrations of the marker in the normal state). In terms of quantity, the leading role was played by Cardiobacterium hominis.