343 Background: Bacillus Calmette-Guerin (BCG) therapy has already been established as a treatment for muscle noninvasive bladder cancer. Although there are several reports indicating the effectiveness of BCG perfusion therapy for the upper urinary tract urothelial carcinoma in situ(CIS), it is not well established yet. We conducted a retrospective study to assess the long-term effects of BCG perfusion therapy for the upper urinary tract CIS. Methods: Thirty-one subjects (24 male, 7 female) who received BCG perfusion therapy for the upper urinary tract CIS from December 1997 to December 2013 were enrolled. 11 subjects had the entire urinary tract CIS, 8 had bilateral, 12 had unilateral CIS of the urinary tract. The average period of observation was 49.9 months (ranging from 5 to 196 months), and the average subject age was 74.8 years (ranging from 56 to 90 years). We used a double-J catheter for 22 cases, a transvesical single-J catheter whose curl was positions in an upper calyx for 8 cases, and a straight ureteral catheter inserted for ureterocutaneostomy for 1 case. We used 80 mg of BCG for the first five cases, 40 mg for the late 26 cases. Urine cytology was performed to assess the treatment validity. Results: Of the 31 cases, the treatment protocol was completed in 27 cases. Urine cytology tests became negative in 25 of the 31 subjects (80.7%) who underwent upper urinary tract perfusion. Among these 22 subjects who had negative tests, 8 subjects had a recurrence in their upper urinary tracts. Side effects were observed in 28 subjects (90.3%), and the most common side effect was bladder irritation. Localized renal tuberculosis, which was successfully treated with conservative therapy, was seen in two cases. Conclusions: BCG perfusion therapy for the upper urinary tract CIS is effective. However, severe side effects are possible, and careful observation is essential while using this therapy.