Objective Fungal peritonitis (FP) is a serious complication of continuous ambulatory peritoneal dialysis (CAPD), being associated with significant morbidity and mortality. The role of nystatin prophylaxis during antibiotic therapy in the prevention of FP remains controversial, especially in programs with a modest or low baseline FP rate. The aim of the present study was to evaluate the effect of nystatin prophylaxis on the occurrence of FP in programs with a relatively modest baseline FP rate. Patients and Methods Incident and prevalent patients receiving CAPD between April 1995 and April 2005 at our center were included and divided into 2 groups. The control group included 320 patients (total follow-up 8875 patient-months) being treated without nystatin before October 1999; the nystatin group included 481 patients (total follow-up 13725 patient-months) being treated after October 1999. Nystatin tablets (500000 units, 4 times per day) were given orally during whatever use of antibiotics to cover the whole course of antibiotic therapy. Occurrence of FP and antibiotic-related FP (AR-FP) in patients with and without nystatin prophylaxis was compared. Results The two groups were of similar age but the nystatin group had a significantly higher percentage of diabetics. In addition, the nystatin group had a higher proportion of patients using disconnecting twin-bag exchange systems and had a significantly lower peritonitis rate compared with the control. There were 13 and 14 episodes of FP in the nystatin and control groups respectively. The fungal peritonitis rate of the nystatin group was slightly lower than that of the control group (0.011 vs 0.019 per patient-year) but it did not reach statistical significance. There was, however, a significant decrease in the incidence and proportion of AR-FP in the nystatin group compared with the control group, which persisted even after adjustment for the peritonitis rate. Kaplan–Meier analysis further demonstrated significantly better AR-FP-free survival in the nystatin group compared with the control group. No significant side effects were observed for nystatin. Subgroup analyses in patients of the 2 different connecting systems revealed a similar but nonsignificant trend toward reduction of AR-FP in patients given nystatin prophylaxis. Conclusion Oral nystatin prophylaxis might prevent the occurrence of AR-FP in CAPD patients, resulting in a trend toward reduction in the incidence of FP even in programs with a modest baseline FP rate. A large scale, prospective, randomized controlled trial is needed to further examine this issue.