At our community teaching hospital between August 1994 and August 1995, Candida glabrata accounted for 14% of all Candida isolates and for 31% of urinary Candida isolates. The culture site was urine for 68% of C. glabrata isolates compared to 30% of all Candida isolates (p < 0.001, chi 2). To study the association between C. glabrata and isolation from the urine, we analyzed all available C. glabrata urinary isolates over a 3-month period (23 isolates from 20 patients) using electrophoretic karyotyping, random amplified polymorphic DNA analysis, and fluconazole susceptibility testing. Random amplified polymorphic DNA generated eight types, although electrophoretic karyotyping generated 17 types. Combining the two methods resulted in 19 types indicating that urinary C. glabrata strains at our hospital are genetically diverse and the association between C. glabrata and urinary tract isolation does not appear to be due to horizontal transmission of a single or small number of strains. In vitro susceptibility tests showed that C. glabrata isolates from patients receiving fluconazole had significantly higher minimum inhibitory concentrations to fluconazole than those not receiving fluconazole (p < 0.05). Despite a limited number of patients and isolates, our data suggest that selection of less susceptible organisms by the presence of antifungal agents may be an important contributor to increased urinary isolation of C. glabrata from patients in our hospital.