Candida glabrata, has emerged as a major pathogen in HIV-infected patients with oropharyngeal candidiasis. This is mainly due to drug resistance acquired with prophylactic use of fluconazole. However, mechanisms for fluconazole resistance in C. glabrata are not properly understood. Objective: To determine genotypic changes associated with fluconazole exposure in a C. glabrata strain. Methods: C. glabrata ATCC2001 was grown on SDA and resuspended in PBS to reach a cell concentration of 108 cells/ml. The cells were pelleted and grown in 20 ml RPMI broth overnight at 370C, and subsequently exposed to fluconazole MIC concentrations (x1 and x2) for 60 min. Control tests were carried out without the drug. The karyotipic changes in C. glabrata were analyzed with randomly amplified polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP) and, contour-clamped homogenous electric field electrophoresis (CHEF) techniques. Results: 1. C. glabrata treated with (x2) MIC fluconazole demonstrated varying electrophoretic patterns with 6 of 8 primers used with RAPD whereas no changes were seen with (x1) MIC of the drug; 2. RFLP analysis showed changes in the genomic profile (around 700-2500 bp) with 2 of 4 restriction enzymes (Dde I and Hae III) and, 3. CHEF analysis failed to show any positive results. Conclusion: Considering the changes noted in the genotypic profile of the yeast isolate pre-treated with fluconazole, it could be said that long term prophylaxis with this drug may lead to chromosomal instability in C. glabrata. (Supported by the Research Grants Council and the Committee of Research and Conference grants, University of Hong Kong, Hong Kong SAR, and the Outstanding Researcher Award of LPS).