The possibility of using the GC method for express and accurate determination of markers of microorganisms in various biological materials with subsequent calculation of the microorganism titer is shown in the work. At the same time, the data on the composition of microorganisms obtained for each patient, when assessing the overall microecological status, allow the doctor to obtain qualitatively new extensive information for the adoption of adequate antimicrobial and general therapy. There is a high correlation between the contents of markers of that microorganisms in various biological objects for sepsis in infants, which shows the determination of the content of markers does not depend on the object in this pathology.