OBJECTIVE To improve the treatment of pyonephrosis with upper urinary tract calculi (UTC). METHODS A total of 49 UTC patients with pyonephrosis were selected at our hospital during May 2004 to February 2010. Among them, 22 cases were treated with transurethral ureteroscope lithotripsy followed by tube internal drainage while another 27 cases underwent percutaneous nephrolithotomy. RESULTS No such complications as septicemia and septic shock occurred during the first stage of external and internal drainage. The bacteremic symptoms of chill or fever occurred in 3 cases during the second stage of percutaneous nephrolithotomy and pyelolithotomy/ureterolithotomy (11.1%). There were 3 cases of nephrectomy. A follow-up period of 3 months to 5.5 years showed that all 33 cases had a varying degree of recovered renal functions. And there was no nephrectomy. CONCLUSIONS The keys to a successful surgical treatment of pyonephrosis with upper urinary tract calculi are early diagnosis, timely drainage and relief of obstruction. Ureteroscopic lithotripsy, double-J placement and percutaneous nephrostomy drainage are excellent for relieving obstruction. As a safe procedure with minor complications, it creates proper conditions for a second stage operation.