Aim. To detect pathogens that are capable of causing diseases or infections as postoperative complications in children with congenital heart and kidney disease, to be effective at preventing catheter-associated urinary tract infection. Materials and methods. Clinical material served samples of excrement, urine and urinary catheters of Foley (Unomedica) from sixteen children with congenital heart disease, who were being treated at the Almazov Medical Research Center. The isolated strains were classified according to the identification RapID Systems (USA). Antibiotic sensitivity of isolated bacteria was performed by thedisk diffusion method (NICF, Russia). Scanning electron microscopy (SEM) imaging revealed several types of bacterial communities on intraluminal surface of urethral catheter. Escherichia coli strains were tested for presence of virulence genes a-hemolysin: hly А, В, C by real-time PCR testing (using the detecting amplifier DTlite (DNA Technology, Russia). Results. The main microbial agents were isolated in urines samples from 3 of 16 patients were Staphylococcus aureus and E. coli. Gram-positive cocci were found in 56% samples of excrement and Gram-negative in 44% samples. It was found that on intraluminal surface in 10 out of 16 urethral catheter samples mixed microbial cultures were isolated, S. aureus and E. coli were prevailed. Methicillin-resistant strains of S. aureus (MRSA) have been reported in 85% cases. E. coli a-hemolysin (Ыу А, В, C) were identified in 60% strains. SEM examination two samples of urinary catheters revealed actinomyces-like forms of bacteria that were not detected in the primary bacteriological study. Conclusion. Early diagnosis of catheter-associated urinary tract infections in children with congenital heart heart and kidney disease requires a comprehensive approach to setting detecting priorities and selecting the most effective microbiological analysis, and is mandatory to use modem diagnostic methods.