The aim of the present randomized clinical study was to compare the efficacies of photodynamic inactivation (PDI) with nystatin (NST) in terms of prevalence of Candida species in cases with denture stomatitis (DS).Thirty-six patients were randomly divided into two groups; 18 in PDI and 18 in NST. Irradiation was carried out by using the GaA1As diode laser with wavelength, mode of transmission, laser output and energy density were standardized at 660 nm, continuous mode, 100 mW power and 28 J/cm2 respectively. The PDI was applied twice a week, with an interval of at least 48 h among the sessions during four weeks. Topical nystatin oral suspension 100,000 IU was used four times daily for 15 days. The existence of Candida spp. was confirmed by employing the microbiological culture technique. Candida colony counts from the palates and dentures surfaces, quantified as colony forming unit (CFU)/mL, measured at baseline, at the end of treatments (day 15), and at follow-up (days 30 and 60) and the prevalence of Candida spp. were identified in the two groups of treatments.The overall CFU/mL values were higher in the dentures of the patients of both the groups than those from the palates. During all time periods of the study, the CFU/mL values obtained from both NST and PDI groups showed no significant differences. For dentures and palates, a significant reduction in mean CFU/mL values was observed on day 15 compared with baseline (day 0) in both NST and PDI groups. It can be seen that the effect size of treatments was large for the palates of patients in the NST group (1.79) and moderate for the palates of patients in the PDI group (0.63). On the other hand, the effect size was very large for the dentures for both groups (NST group = 3.01; PDI group = 1.58). C. albicans was the most common species on both dentures and palates of patients throughout the study period followed by C. tropicalis and C. glabrata.Out of all the Candida spp., C. albicans showed the highest prevalence among all species. In addition, PDI was equally effective as nystatin for the treatment of DS.