Fifty episodes of oropharyngeal candidiasis in HIV-infected patients were analyzed prospectively in order to evaluate the clinical response to fluconazole. The minimum inhibitory concentrations (MICs) of fluconazole for the Candida strains isolated from the pharynx were correlated with the clinical response. Treatment with fluconazole (100 mg/day) was successful in 86% of the cases. A good clinical outcome followed in 97% of the cases when a strain sensitive to fluconazole was isolated. This figure fell to 22% when the strain was resistant to fluconazole (p < 0.001). The rate of post-treatment colonization was high (87%), and selection of non-albicans Candida species occurred in 23% of the cases. In conclusion, fluconazole treatment for oropharyngeal candidiasis of HIV-infected patients was useful in most cases, but less sensitive non-albicans species can be selected. Most treatment failures were associated with increased MICs of fluconazole for the strains isolated before treatment; therefore, susceptibility testing is recommended as an aid in clinical decision-making for the use of the azole group of drugs.