The article discusses methods for the detection and identification of pathogenic and opportunistic microorganisms in food and feed using express methods and classical microbiology. The calculation of labor and time costs was spend in using the Vidas (mini Vidas) immunofluorescence analyzer, the microbiological analyzer Tempo and the PCR. A brief description of pathogens that can be detected by the above express methods is given. Methods for identifying pathogens using API-systems, a Vitek bacteriological analyzer and MALDI-TOF MS (matrix-activated laser desorption/ionization) are also considered. The prospects for the application and implementation of chromatographic methods for the study of pathogens in food and animal feed are considered on the example of the analysis of microbial markers in human biomaterial. This technique was developed by Professor G. A. Osipov in 1991 and is used in medical research. Additionally, a laboratory program is described that controls all stages of testing from registration of samples to the issuance of research results. The main advantage of software laboratory control (LIMS) is the reduction of time and labor costs for routine work, as well as the reduction of paper workflow with the possibility of its complete replacement.