We investigated the long-term efficacy and safety of intrarenal bacillus Calmette-Guerin (BCG) therapy for carcinoma in situ (CIS) of the upper urinary tract. We retrospectively reviewed the medical records of 9 patients who underwent BCG perfusion therapy for CIS of the upper urinary tract from January 2005 to December 2011 at our institute. All patients were treated by retrograde catheterization using a 6 Fr double- J ureteric stent. BCG at half the dose (40.5 mg or 40 mg) in 40ml saline was instilled into the bladder weekly for 6 or 8 weeks as one course. The mean follow-up period was 32.7 months (range 4-75 months). In all patients (100%), cytology became negative after one course of BCG perfusion and 8 patients (88. 9%) remained disease-free for a median follow-up of 35.1 months. Among these 9 patients, 1 patient showed recurrence after 6 months of the first BCG therapy. The patient received a second course of BCG therapy, but the patient developed invasive tumor and distant metastases. Two patients could not continue the treatment due to pyelonephritis. In conclusion, although longer follow up and further experience with treatment for CIS of the upper urinary tract are required, this treatment is considered to be effective and safe.