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Introduction: Due to the extensive use of indwelling stents and catheters in urology, bacterial colonization on these materials is a significant cause of infections in this group of patients. This study aims to investigate and compare the bacterial colonization in urine and in the three zones of the double J (DJ) stent. Methods: Between August 2019 and May 2020, 67 patients (18–78 years old) who underwent DJ stenting were recruited in the study. Surgeries before stenting included transurethral lithotripsy (TUL), percutaneous nephrolithotomy (PCNL), or diagnostic ureteroscopy. Before stenting, sterile urine samples were collected, and urinary cultures were performed, and the same procedure was done after removal of the DJ stents. DJ stent cultures were also performed. Results: 61 patients were analyzed. The mean age of all patients was 53 ± 16 years. The mean time of DJ installation in all patients was 27.6 ± 6.7 days (14–43 days). In these three parts of the DJ, 70.5%, 67.2%, and 72.1% of patients were without a colony, respectively. The microorganism distribution is approximately the same in the lower and upperparts, and Escherichia coli has the highest frequency (11.5%). The odds ratio (OR) of contamination was significantly lower in men than in women, but overweight and diabetes were not associated. Conclusion: The severity and pattern of bacterial colonization are not significantly different in the proximal, distal, and middle parts of the DJ stent. [ABSTRACT FROM AUTHOR]