Carcinoma in situ and urothelial tumors of the upper urinary tract become problematic in cases of bilateral occurrence or solitary kidney. Perfusions with bacillus Calmette-Guerin (BCG) have been reported beneficial, however, only long-term results will determine the validity of this treatment. We retrospectively evaluated the results of BCG therapy for upper urinary tract disease in 37 patients. All 37 patients had undergone previous surgical treatment for urothelial cancer, had a positive cytology or biopsy for upper urinary tract cancer and were ineligible for radical nephroureterectomy with a bladder cuff. After placement of a 10Fr nephrostomy tube with the patient under local anesthesia 6 weekly perfusions of BCG were administered after radiological documentation of unhindered flow from the renal pelvis to the bladder or urinary diversion. A total of 25 renal units were treated with curative intent for carcinoma in situ and 16 renal units were treated for Ta or higher urothelial tumors in an adjuvant setting after endoscopic resection. In 37 patients 41 renal units were treated with BCG perfusions and were followed for a median of 42 months (range 8 to 137). In 1 patient BCG inflammation and in 2 others severe septicemia developed after the first perfusion. There was no tumor seeding along the nephrostomy tract in any patient. BCG perfusion therapy did not alter renal function. Overall median survival was 42 months (range 1 to 137), median recurrence-free survival was 21 months (1 to 137) and progression-free survival was 34 months (1 to 118). Of the 37 patients 14 (38%) died of urothelial cancer, 11 of other causes (29%) and 12 (33%) are alive. BCG perfusion therapy of the upper urinary tract for papillary tumors or carcinoma in situ is a valid treatment option with acceptable side effects for patients not amenable to conventional radical surgical therapy. BCG therapy of upper urinary tract urothelial tumors may prevent patients from requiring dialysis and provides cure in those with carcinoma in situ of the upper urinary tract. In this negatively selected patient population BCG buys time for some but does not provide cure except for carcinoma in situ.