Abstract: Objective To explore the clinical value of renal pelvis urine culture and stone culture in the diagnosis and treatment of infection after percutaneous nephrolithotomy (PCNL). Methods A total of 88 patients who received PCNL in the Affiliated Hospital of Xuzhou Medical University from May 2017 to December 2019 were enrolled and their clinical data were retrospectively analyzed. All patients underwent preoperative mid-stream urine culture, intraoperative renal pelvis urine culture and stone culture. The relationship between culture results and postoperative systemic inflammatory response syndrome (SIRS) and septic shock was analyzed. Results There were 88 patients, including 54 men and 34 women. There were 19 patients (21.6%) with positive mid-stream urine culture and 14 patients (15.9%) with positive renal pelvis urine culture/stone culture. The most common bacteria were Escherichia coli and Proteus mirabilis respectively. For patients with negative mid-stream urine culture, 10 patients (14.5%) were positive in renal pelvis urine culture/stone culture. Thirty patients developed SIRS and five developed septic shock after PCNL. Female patients were more likely to develop SIRS after PCNL than mal patients (50.0% vs 24.5%, P=0.012). The positive rate of renal pelvis urine culture/stone culture in SIRS patients was higher than that in non-SIRS patients, which was 26.7% and 10.3% respectively (P=0.066). In the shock group, 40% patients were positive in renal pelvis urine culture/stone culture, which was significantly higher than that in the non-shock group (13.3%, P=0.027). Conclusions Positive renal pelvis urine culture/stone culture is of importance to predict postoperative SIRS and septic shock. Routine renal pelvis urine and stone culture have positive significance for the diagnosis and treatment of infection after PCNL.