The effects of short-course antifungal regimens on funguria were studied in 180 hospitalized adults who did not have ascending urinary or deep fungal infections but did have > 1,000 cfu of yeast/mL in two consecutive urine cultures. Before treatment, efforts were made to eliminate factors conducive to funguria. No additional interventions were implemented in the management of the control group (group A), whereas five experimental groups received short-course therapy as follows: oral administration of fluconazole (group B); single-dose intravenous administration of amphotericin B (group C); and intermittent bladder irrigation with amphotericin B at low, medium, and high concentrations (groups D, E, and F, respectively). Urine was cultured on days 1 and 7 after antifungal treatment. The rate of spontaneous clearance of funguria in the control group was 40.0%. Rates of clearance in experimental groups B through F were 58.6%, 55.2%, 82.1% (P < .01), 86.7% (P < .001), and 83.3% (P < .001), respectively, on day 1 and 77.3% (P < .01), 72.0% (P < .05), 42.9%, 68.4%, and 68.2% (P < .05), respectively, on day 7. The decrement in yeast count was 60.8% for the control group. Decrements for experimental groups B through F were 80.5%, 74.2%, 94.2% (P < .01), 86.7% (P < .05), and 95.3% (P < .001), respectively, on day 1 and 85.5% (P < .05), 80.7%, 75.7%, 87.9% (P < .05), and 76.4%, respectively, on day 7. We conclude that (1) the systemic regimens tested result in prolonged clearance of funguria and prompt decreases in yeast count and (2) local irrigation with amphotericin B has prompt but short-lived effects regardless of the drug concentration used.