Bacteriophages are highly efficient in treatment of intestinal and respiratory infections caused by community-acquired antibiotic-resistant pathogens. However, mass production of bacteriophages does not consider a rapid turnover of circulating strains causing healthcare-associated infections, formation of anti-phage immunity, the focus of infection in human body, phage pharmacokinetics, and a number of other issues. Therefore, we developed an original algorithm for personalized phage therapy which includes three consecutive stages: 1) determination of bacterium sensitivity to a number of widely applied bacteriophage strains using spot test and modified Gratia’s assay; 2) measurement of neutralizing anti-phage IgG in the patients’ serum utilizing enzyme-linked immunosorbent assay and neutralization test; 3) personalized selection of the phage strain for therapy including assessment of the optimal route of delivery and phage pharmacokinetic properties. Implementation of aforementioned algorithm for patients with healthcare-associated infections in intensive care units resulted in 40% increase in efficiency of phage therapy (up to 72 per cent).