Objectives: this study investigated the efficacy of denture microwave disinfection compared with that of topical antifungal medication in reducing Candida colony counts on the palates and dentures of diabetic patients. Methods: forty diabetic patients with denture stomatitis were selected and instructed to scrub their dentures with coconut soap and water four times a day and soak it in water overnight. Patients were randomly divided into two groups of treatment (n=20): Control group (CG) patients received topical antifungal medication (Nystatin oral suspension 100.000 UI/mL) 4x/daily for 14-days; Test group (TG) patients had their maxillary denture immersed in water and microwaved (650W/3min) 3x/weekly for 14-days. Mycological samples were taken from the tissue side of dentures and palatal mucosa before treatment (day-0), after starting treatment (14-days) and follow-up (30-days). Samples were cultured in SDA′s plates and incubated (30°C, 2 days). The effectiveness of treatments was evaluated by quantification of Candida colony counts (cfu/mL). Data were analyzed using Kruskall-Wallis test followed by Dunn's post hoc test (P≤.05). Results: After treatment, patients in CG presented a significant decrease (P<.05) in cfu/mL of Candida on palatal mucosa (from 3.6x102 to 2x101 cfu/mL). The cfu/mL of Candida on dentures was significantly reduced (P<.05) after treatment for both groups (CG- from 2.9x105 to 3.3x104 cfu/mL; TG- from 3x104 to 1.1x104 cfu/mL). When the two treatment groups were compared, there were no significant differences in cfu/mL that colonized palatal mucosa and dentures in day-0, 14-days and 30-days. Conclusion: microwaving dentures demonstrated to be as effective as Nystatin in decreasing Candida colonies present in complete dentures from diabetic patients with denture stomatitis. GRANT: FAPESP 2006/02842-5 and 2007/03895-8; CNPq 470337/2007-9.