The spread of drug resistant bacterial pathogens and their increased ability to survive in the environment combined with the lack of new classes of antibiotics causes the need to look for new ways to treat bacterial infections. One suitable alternative is phage therapy. For the effective treatment of infections caused by Staphylococcus aureus strains, which belong to ESKAPE group, the most promising is the application of polyvalent Twort‐like bacteriophages with broad-host range and similarly podoviruses. Although, the genomic properties of phages are well-studied, new findings are emerging on the pharmacokinetic profiling of phage drugs. The major factors relevant for the therapeutic use of phages include: i) optimal dosing, ii) duration of exposure to phages, iii) absence of genes for toxins and virulence factors in phage genome, and iv) selection of suitable phages depending on the infection agent. Currently, there is also lack of methods for capturing and monitoring bacteriophages in clinical material. The aim of our study is to develop a sufficiently sensitive method for the detection and quantification of phage particles in different types of clinical material during phage therapy based on qPCR, specially designed luminescent (upconversion, UCNPs) and metal nanoparticles4and magnetic particles.