Decrease in macroorganism reactivity and immunological potential of the urogenital tract epithelium is believed to be the cause of ineffectiveness of standard therapy of mixed infections of the urogenital tract. The study was aimed at improving the therapy of patients with combined herpetic and papillomavirus infection of the genitals. Material and methods. We examined and treated 30 patients (18 females and 12 males) with combined recurrent bacterial and viral infection of the urogenital tract. The state of the microbiome of the lower genito-urinary tract was studied before and after complex therapy including the preparation of the antimicrobial peptide complex. Results. The results showed that the use of the preparation of the antimicrobial peptide complex at the dose of 1 rectal suppository per day in combination with standard therapy proved to be clinically effective in 93.3% of patients.