Background: Denture stomatitis, also known as atrophic candidiasis, is the most common fungal infection in elder patients and in those who wear dentures. This condition is usually asymptomatic, although it can be associated with burning, bleeding, an unpleasant taste. Even though several microorganisms can cause this condition, most studies showed that Candida albicans and the ill-fitting dentures promote the development of this condition. Several studies have attempted to incorporate antifungal agents to tissue conditioner for prevention of plaque formation and treatment of denture stomatitis. Aim of the study: To compare Fluconazole and Nystatin incorporated into Tissue Conditioner for denture stomatitis. Materials and methods: The present study was conducted in the Department of Prosthodontics of the Dental institution. For the study sample, we obtained clinical isolates of Candida albicans (ATCC 10231), from the Department of molecular microbiology of medical institute, to use as test organisms for the current experimental study. Candida albicans was cultured onto Sabouraud dextrose agar plate and incubated at 37ºC for 3 days. A colony from the stock culture was then diluted in 2 ml sterile saline and a suspension of 1×106 CFU/ml was prepared. Results: We observed that that Nystatin 5% solution was the most efficient for inhibiting attachment and colonization of C. albicans. Fluconazole 5% solution is partially effective efficient for inhibiting attachment and colonization of C. albicans. The control solution was least effective with highest Candida density seen in control solution. Conclusion: Within the limitations of the present study, it can be concluded that the incorporation of Nystatin into the tissue conditioner is more efficacious than Fluconazole for denture stomatitis. Keywords: Denture stomatitis, Nystatin, Tissue conditioners