Persistent funguria may cause significant morbidity and potential mortality. Both amphotericin B as a urinary irrigant and systemic fluconazole have been effective therapeutic agents. In cases when amphotericin supplies are limited by manufacturing shortfall or when renal insufficiency lessens urine levels of fluconazole, other antifungal treatment modalities may be necessary. Fluconazole used as a genitourinary irrigant has been reported as an effective antifungal bladder irrigant. In this study, 6 patients were treated with fluconazole bladder irrigant. Four patients had a complete response, 1 patient required a second course of treatment, and 1 patient did not respond. Further study is necessary to determine whether fluconazole is effective in the management of candiduria caused by non-albicans species. Amphotericin B should remain in the armamentarium of the treating physician. Present-day drug costs are comparable.