The study aims to investigate the risk factors associated with the adverse outcome of residual stones after percutaneous nephrolithotomy (PCNL) for upper urinary tract calculi. 233 patients who underwent PCNL for upper urinary tract calculi and had postoperative residual stones were included. The adverse outcome of residual stones was defined as an increase in postoperative residual stone diameter or the recurrence of stone-related symptoms. The risk factors were analyzed from the patients’ records and the presence or absence of the adverse outcome. The factors examined were gender, age, location of the stone, the maximum diameter of stone, serum creatinine, calcium in blood, urine PH, size of residual stone, urine culture, hypertension, and diabetes. In addition, the difference was examined for stone composition and the type of bacteria in the urine culture. An adverse outcome of residual stones developed in 125 of 233 patients. Univariate analysis showed that the size of postoperative residual stones and positive urine culture were the risk factors for the adverse outcome. The probability of adverse outcome increased by about 1.694 times, when the diameter of residual stones increased by 1mm. The probability of adverse outcome in patients with positive urine culture was about 2.111 times higher than those with negative urine culture. However, other factors analyzed were not related to the adverse outcome of residual stone. In conclusion, longer diameter of residual stones and positive urine culture are risk factors associated with the adverse outcome of residual stones after PCNL for upper urinary tract calculi.