Objectives: This randomized clinical trial compared the clinical and mycological efficacy of Photodynamic Therapy (PDT) with that of topical antifungal therapy (nystatin oral suspension) for the treatment of denture stomatitis (DS). Methods: Forty DS patients were randomly assigned to one of two groups of 20 subjects each; NYS group: patients received topical treatment with nystatin (100,000-IU) four times daily for 15 days; PDT group: denture and palate of patients were sprayed with 500-mg/L of Photogem® and, after 30-min of incubation, illuminated by LED light at 455 nm (light fluences of 37.5- and 122-J/cm2, respectively) three times a week for 15 days. Mycological cultures from oral swabs samples taken from dentures and palates and standard photographs of the palates were performed at baseline (day 0), at the end of the treatment (day 15) and at the follow-up (days 30, 60 and 90). Colonies on Sabouraud Dextrose Agar (37°C, 48-h) were quantified and the ln(CFU/mL) values were statistically analyzed by ANOVA and Tukey tests (α=0.05). The severity of inflammation of the palate in the photographs was evaluated according to Newton's classification. Results: Both treatments reduced significantly the CFU/mL values at the end of the treatments (day 15) and on day 30 of the follow-up period (P<0.05). NYS and PDT groups showed a rate of clinical success (cure or improvement of the palatal inflammation) of 53 and 45%, respectively, on day 15. At the follow-up period, recurrence of the palatal inflammation was observed in 75 and 78% of the patients who had clinical success respectively in the NYS and PDT groups. Conclusion: PDT appears to be an alternative method for the treatment of DS. Grant: FAPESP 2005/02193-4 and 2005/03226-3.