The purpose of this study was to compare the postoperative course of patients with positive stone culture (SC) to patients with sterile SC, and to analyze the predictors for post percutaneous nephrolithotomy (PCNL) sepsis; and to describe the type and resistance patterns of bacteria responsible for post PCNL sepsis. From a cohort of 206 consecutive patients undergoing PCNL, we identified 45 patients with a positive SC (group A) and compared them to patients with a sterile SC (group B). Association between different groups was assessed using Chi square, two-tailed Student's t test and Mann-Whitney U test, as appropriate. Twenty-three patients had postoperative sepsis and regression analysis was performed to identify clinical variables associated with sepsis. Demographics, stone load and hospitalization time were similar in both groups. Postoperative sepsis developed in 31.1% of patients in group A compared to 5.9% in group B. In multivariate analysis, only positive SC was an independent risk factor for postoperative sepsis (OR 6.894, 95% CI 2.31-20.59, P = 0.001). All patients responded well to treatment with no septic complications. Enterococci were the prevalent organism (29.4%) in patients with a positive SC. Quinolone resistance was high in both gram negative and gram positive bacteria. Patients with an infected stone are at high risk to develop postoperative sepsis despite standard preoperative antibiotic preparation. SC is important to direct further treatment as almost half of patients with positive SC have a discordant or sterile urine culture. Determining the prevalent bacteria and resistance patterns in SC can aid the selection of empiric antibiotic therapy in high-risk patients.