Topical antibiotic and antiseptic agents have been documented to reduce exit-site infection (ESI) and peritonitis in PD. The aim of this randomized controlled study was to evaluate the efficacy of polyhexanide in the prevention of ESI and peritonitis. Patients were excluded if they had active infection, > 18 years of age, ESI and peritonitis within the previous 4 weeks, received PD for less than 3-months and history of allergy to either drug. All patients were followed up until catheter removal, death, switch to dialysis, transplantation or the end of the study. ESI, tunnel infection, peritonitis, catheter removal and microorganism cause of catheter-related infection were recorded prospectively during clinic follow-up. A total of 88 patients (41 povidone-iodine group; 47 polyhexanide group) were enrolled with a total follow-up duration of 480 and 555 patient-months for povidone-iodine and alternating group, respectively. There were no significant differences in the age, sex, BMI, time of PD, rate of DM, and S. aureus carriage state. A total of 8 ESI and 25 peritonitis episodes were detected during the study. ESI and peritonitis rates tended to be lower in polyhexanide group compared with the povidone-iodine group (0.06 episodes/patient-year vs. 0.12 episodes/patient-year; 0.26 episodes/patient-year vs. 0.32 episodes/patient-year, respectively), but were not significant statistically. Moreover, catheter removal was similar in both groups (0.04 / patient-year vs. 0.05 / patient-year). Polyhexanide is efficient and safe for the prevention of ESI and peritonitis and it may be used as an alternative procedure for the care of healthy exit sites.