Antimicrobial properties of structural components and vital activity products of probiotic strains of Lactobacillus rhamnosus GG and Saccharomyces boulardii against the individual representatives of pathogenic agents of diphtheria and nonpathogenic corynebacteria were investigated in vitro and in vivo. Disintegrats (structural components) were obtained with low–frequency ultrasonic treatment of probiotic cells of Lactobacillus rhamnosus GG or Saccharomyces boulardii. Metabolites were obtained using the author’s method by cultivating lactobacteria and saccharomycetes in their own disintegrates, and their combination – in the disintegrate of lactobacteria. In tests in vitro, the filtrates of lactobacteria metabolites compounds, if applied in a sowing test-culture dose (0,5 units on the McFarland scale, diluted 10 times) within two hours of exposure, manifested bactericidal properties (100%) for toxicogenic corynebacteria (n=10). The filtrate of saccharomycetes structural components and metabolites showed less activity (80%) on vitality indicators of toxic Corynebacterium genus representatives (n = 10). The combined cultivation of L. rhamnosus GG and S. boulardii in the ultrasound disintegration of probiotic lactobacteria cells led to increase in antimicrobial activity of a combination of metabolites for pathogenic corynebacteria. In tests in vivo on guinea pigs, antimicrobial activity of lactobacteria metabolites and a combination of lactobacteria with saccharomycetes metabolites was established. Also, their efficacy for local treatment (three times a day during a week) of diphtheria infection of the eye was proved. The results obtained, can be used for development on the basis of Lactobacillus and Saccharomyces antimicrobial structural–metabolites complexes for prevention of asymptomatic forms of diphtheria infection, sanitation of diphtheria carriers and an additional local treatment of diphtheria of the eye.